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Eugene Koonin

Research Profile

Phenomena

Evolution, Molecular

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Publications

TOP 3
Toni Gabaldón; Eugene V Koonin
Functional and evolutionary implications of gene orthology.
Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Comparative genomics of defense systems in archaea and bacteria.
David M Kristensen; Arcady R Mushegian; Alison S Waller; Takuji Yamada; Peer Bork; Eugene V Koonin
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.

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All Publications

2013: Toni Gabaldón; Eugene V Koonin
Functional and evolutionary implications of gene orthology.
Nature reviews. Genetics 2013;14(5):360-6.
2013: Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Comparative genomics of defense systems in archaea and bacteria.
Nucleic acids research 2013;41(8):4360-77.
2013: David M Kristensen; Arcady R Mushegian; Alison S Waller; Takuji Yamada; Peer Bork; Eugene V Koonin
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.
Journal of bacteriology 2013;195(5):941-50.
2013: Eugene V Koonin; Armen Y Mulkidjanian
Evolution of cell division: from shear mechanics to complex molecular machineries.
Cell 2013;152(5):942-4.
2013: Eugene V Koonin
Elaborate security TRAINing to fight against expression of genomic junk.
Cell cycle (Georgetown, Tex.) 2013;12(4):553-4.
2013: David Managadze; Igor B Rogozin; Svetlana A Shabalina; Yuri I Wolf; Alexander E Lobkovsky; Eugene V Koonin
The vast, conserved mammalian lincRNome.
PLoS computational biology 2013;9(2):e1002917.
2013: David Prangishvili; Eugene V Koonin; Mart Krupovic
Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea.
Biochemical Society transactions 2013;41(1):443-50.
2013: Mark Young; Benjamin Bolduc; Francisco F Roberto; Daniel P Shaughnessy; Yuri I Wolf; Eugene V Koonin
Reply to "codon usage frequency of RNA virus genomes from high-temperature acidic-environment metagenomes".
Journal of virology 2013;87(3):1920-1.
2013: Ben Busby; David M Kristensen; Eugene V Koonin
Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens.
Environmental microbiology 2013;15(2):307-12.
2013: Eugene V Koonin; Laura F Landweber; David Lipman
Biology direct: celebrating 7 years of open, published peer review.
Biology direct 2013;8(1):11.
2013: Mircea Podar; David E Graham; Eugene V Koonin; Kira S Makarova; Yuri I Wolf; Anna-Louise Reysenbach
Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.
Biology direct 2013;8(1):9.
2013: Valerian V Dolja; Eugene V Koonin
The closterovirus-derived gene expression and RNA interference vectors as tools for research and plant biotechnology.
Frontiers in microbiology 2013;4():83.
2013: Pere Puigbò; Yuri I Wolf; Eugene V Koonin
Seeing the Tree of Life behind the phylogenetic forest.
BMC biology 2013;11():46.
2013: Natalya Yutin; Didier Raoult; Philippe Colson; Eugene V Koonin
Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family.
Virology journal 2013;10():106.
2013: Alexander E Lobkovsky; Yuri I Wolf; Eugene V Koonin
Gene frequency distributions reject a neutral model of genome evolution.
Genome biology and evolution 2013;5(1):233-42.
2013: Eugene V Koonin; Miklos Csuros; Igor B Rogozin
Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes.
Wiley interdisciplinary reviews. RNA 2013;4(1):93-105.
2012: J-C Lagier; Marie Maraninchi; M Million; I Pagnier; Fabrice Armougom; Fadi Bittar; Ghislain Fournous; G Gimenez; P Hugon; Eugene V Koonin; Bernard La Scola; C Robert; J-F Trape; Didier Raoult
Microbial culturomics: paradigm shift in the human gut microbiome study.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2012;18(12):1185-93.
2012: Christelle Desnues; Ghislain Fournous; Priscilla Jardot; Eugene V Koonin; Bernard La Scola; Sonia Monteil; Saïd Azza; Angélique Campocasso; Catherine Robert; Natalya Yutin; Didier Raoult
Provirophages and transpovirons as the diverse mobilome of giant viruses.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(44):18078-83.
2012: Armen Y Mulkidjanian; Andrew Yu Bychkov; Daria V Dibrova; Michael Galperin; Eugene V Koonin
Open questions on the origin of life at anoxic geothermal fields.
Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life 2012;42(5):507-16.
2012: Daria V Dibrova; Michael Galperin; Eugene V Koonin; Michail Y Chudetsky; Armen Y Mulkidjanian
The role of energy in the emergence of biology from chemistry.
Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life 2012;42(5):459-68.
2012: Eugene V Koonin
A half-century after the molecular clock: new dimensions of molecular evolution.
EMBO reports 2012;13(8):664-6.
2012: Benjamin Bolduc; Eugene V Koonin; Francisco F Roberto; Daniel P Shaughnessy; Yuri I Wolf; Mark Young
Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs.
Journal of virology 2012;86(10):5562-73.
2012: Armen Y Mulkidjanian; Andrew Yu Bychkov; Daria V Dibrova; Michael Y Galperin; Eugene V Koonin
Origin of first cells at terrestrial, anoxic geothermal fields.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(14):E821-30.
2012: Nobuto Takeuchi; Yuri I Wolf; Kira S Makarova; Eugene V Koonin
Nature and intensity of selection pressure on CRISPR-associated genes.
Journal of bacteriology 2012;194(5):1216-25.
2012: Sonia Paytubi; Catherine H Botting; Shirley Graham; Eugene V Koonin; Huanting Liu; Kira S Makarova; Stephen McMahon; James H Naismith; Malcolm F White
Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(7):E398-405.
2012: Aurore Gorlas; Eugene V Koonin; Daniel Prieur; Nadège Bienvenu; Claire Geslin
TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus.
Environmental microbiology 2012;14(2):503-16.
2012: Yuri I Wolf; Natalya Yutin; Kira S Makarova; Eugene V Koonin
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.
Biology direct 2012;7():46.
2012: Alexander E Lobkovsky; Eugene V Koonin
Replaying the tape of life: quantification of the predictability of evolution.
Frontiers in genetics 2012;3():246.
2012: Ariel D Weinberger; Yuri I Wolf; Michael S Gilmore; Alexander E Lobkovsky; Eugene V Koonin
Viral diversity threshold for adaptive immunity in prokaryotes.
mBio 2012;3(6):e00456-12.
2012: Niyaz Yoosuf; Natalya Yutin; Saïd Azza; Philippe Colson; Thomas Klose; Bernard La Scola; Isabelle Pagnier; Didier Raoult; Catherine Robert; Michael G Rossmann; Svetlana A Shabalina; Jimson Wong; Eugene V Koonin
Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage.
Genome biology and evolution 2012;4(12):1324-30.
2012: Sagi Snir; Yuri I Wolf; Eugene V Koonin
Universal pacemaker of genome evolution.
PLoS computational biology 2012;8(11):e1002785.
2012: Yuri I Wolf; Eugene V Koonin
A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes.
Genome biology and evolution 2012;4(12):1286-94.
2012: Kira S Makarova; Vivek Anantharaman; L Aravind; Eugene V Koonin
Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes.
Biology direct 2012;7():40.
2012: Didier Raoult; Eugene V Koonin
Microbial genomics challenge Darwin.
Frontiers in cellular and infection microbiology 2012;2():127.
2012: Natalya Yutin; Eugene V Koonin
Proteorhodopsin genes in giant viruses.
Biology direct 2012;7():34.
2012: Eugene V Koonin; Yuri I Wolf
Evolution of microbes and viruses: a paradigm shift in evolutionary biology?
Frontiers in cellular and infection microbiology 2012;2():119.
2012: Liran Carmel; Eugene V Koonin; Stella Dracheva
Dependencies among editing sites in serotonin 2C receptor mRNA.
PLoS computational biology 2012;8(9):e1002663.
2012: Eugene V Koonin
Does the central dogma still stand?
Biology direct 2012;7():27.
2012: Natalya Yutin; Eugene V Koonin
Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes.
Virology journal 2012;9():161.
2012: Maud M Swanson; Lesley Torrance; Peter J Cock; David W Hopkins; Eugene V Koonin; Kira S Makarova; Brian Reavy; Michael E Taliansky
Novel bacteriophages containing a genome of another bacteriophage within their genomes.
PloS one 2012;7(7):e40683.
2012: Eugene V Koonin; Valerian V Dolja
Expanding networks of RNA virus evolution.
BMC biology 2012;10():54.
2012: Natalya Yutin; Eugene V Koonin; Pere Puigbò; Yuri I Wolf
Phylogenomics of prokaryotic ribosomal proteins.
PloS one 2012;7(5):e36972.
2012: Igor Rogozin; Liran Carmel; Miklos Csuros; Eugene V Koonin
Origin and evolution of spliceosomal introns.
Biology direct 2012;7():11.
2012: Natalya Yutin; Eugene V Koonin
Archaeal origin of tubulin.
Biology direct 2012;7():10.
2012: Pere Puigbò; Yuri I Wolf; Eugene V Koonin
Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.
Methods in molecular biology (Clifton, N.J.) 2012;856():53-79.
2012: Kira S Makarova; Eugene V Koonin; Zvi Kelman
The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes.
Biology direct 2012;7():7.
2011: Valerian V Dolja; Eugene V Koonin
Common origins and host-dependent diversity of plant and animal viromes.
Current opinion in virology 2011;1(5):322-31.
2011: Kira S Makarova; Sagi Snir; Yuri I Wolf; Eugene V Koonin
Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.
Journal of bacteriology 2011;193(21):6039-56.
2011: James O McInerney; John F Allen; John M Archibald; Michael Y Galperin; Eugene V Koonin; Nick Lane; William F Martin; T Martin Embley
Planctomycetes and eukaryotes: a case of analogy not homology.
BioEssays : news and reviews in molecular, cellular and developmental biology 2011;33(11):810-7.
2011: Kojiro Takeda; Nam K Tonthat; Weijun Xu; Mitsuhiro Yanagida; Tiffany Glover; Eugene V Koonin; Maria A Schumacher
Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(41):16950-5.
2011: Eugene V Koonin
Obituary: Walter Fitch and the orthology paradigm.
Briefings in bioinformatics 2011;12(5):377-8.
2011: Miklos Csuros; Igor Rogozin; Eugene V Koonin
A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes.
PLoS computational biology 2011;7(9):e1002150.
2011: Tatiana G Senkevich; Eugene V Koonin; Bernard Moss
Vaccinia virus F16 protein, a predicted catalytically inactive member of the prokaryotic serine recombinase superfamily, is targeted to nucleoli.
Virology 2011;417(2):334-42.
2011: David M Kristensen; Arcady R Mushegian; Yuri I Wolf; Eugene V Koonin
Computational methods for Gene Orthology inference.
Briefings in bioinformatics 2011;12(5):379-91.
2011: Eugene V Koonin
Are there laws of genome evolution?
PLoS computational biology 2011;7(8):e1002173.
2011: Eugene V Koonin; Pere Puigbò; Yuri I Wolf
Comparison of phylogenetic trees and search for a central trend in the "forest of life".
Journal of computational biology : a journal of computational molecular cell biology 2011;18(7):917-24.
2011: Kira S Makarova; Daniel H Haft; Rodolphe Barrangou; Stan J J Brouns; Emmanuelle Charpentier; Philippe HORVATH; Sylvain Moineau; Francisco J M Mojica; Yuri I Wolf; Alexander F Yakunin; John van der Oost; Eugene V Koonin
Evolution and classification of the CRISPR-Cas systems.
Nature reviews. Microbiology 2011;9(6):467-77.
2011: Ana P G Silva; Maria Chechik; Robert T Byrne; David G Waterman; C Leong Ng; Eleanor J Dodson; Eugene V Koonin; Alfred A Antson; Callum Smits
Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains.
Structure (London, England : 1993) 2011;19(5):622-32.
2011: Madhusudhan Srinivasan; Preeti Mehta; Yao Yu; Evelyn Prugar; Eugene V Koonin; A Wali Karzai; Rolf Sternglanz
The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A.
The EMBO journal 2011;30(5):873-81.
2011: 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 computational biology 2011;7(3):e1002024.
2011: Valera V Peremyslov; Todd C Mockler; Sergei A Filichkin; Samuel E Fox; Pankaj Jaiswal; Kira S Makarova; Eugene V Koonin; Valerian V Dolja
Expression, splicing, and evolution of the myosin gene family in plants.
Plant physiology 2011;155(3):1191-204.
2011: Zhanna Berdygulova; Lars F Westblade; Laurence Florens; Eugene V Koonin; Brian T Chait; Erlan Ramanculov; Michael Washburn; Seth A Darst; Konstantin Severinov; Leonid Minakhin
Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45.
Journal of molecular biology 2011;405(1):125-42.
2011: Kira S Makarova; Yuri I Wolf; L Aravind; Eugene V Koonin
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems.
Biology direct 2011;6():38.
2011: Maureen A O'Malley; Eugene V Koonin
How stands the Tree of Life a century and a half after The Origin?
Biology direct 2011;6():32.
2011: Philippe Colson; Ghislain Fournous; Bernard La Scola; Didier Raoult; Catherine Robert; Svetlana A Shabalina; Natalya Yutin; Eugene V Koonin
Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes.
Genome biology and evolution 2011;3():737-42.
2011: Diana Chernikova; Miklós Csürös; Eugene V Koonin; Sam Motamedi; Igor B Rogozin
A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes.
Biology direct 2011;6():26.
2011: Mohan Babu; Natalia Beloglazova; Robert Flick; Chris Graham; Tatiana Skarina; Boguslaw Nocek; Alla Gagarinova; Oxana Pogoutse; Greg Brown; Andrew Binkowski; Sadhna Phanse; Andrzej Joachimiak; Eugene V Koonin; Alexei Savchenko; Andrew Emili; Jack Greenblatt; Aled M Edwards; Alexander F Yakunin
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.
Molecular microbiology 2011;79(2):484-502.
2010: Eugene V Koonin
The wonder world of microbial viruses.
Expert review of anti-infective therapy 2010;8(10):1097-9.
2010: Eugene V Koonin
New variants of known folds: do they bring new biology?
Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66(Pt 10):1226-9.
2010: Kira S Makarova; Natalya Yutin; Stephen D Bell; Eugene V Koonin
Evolution of diverse cell division and vesicle formation systems in Archaea.
Nature reviews. Microbiology 2010;8(10):731-41.
2010: Michael Galperin; Eugene V Koonin
From complete genome sequence to 'complete' understanding?
Trends in biotechnology 2010;28(8):398-406.
2010: Svetlana A Shabalina; Aleksey Y Ogurtsov; Alexey N Spiridonov; Pavel Novichkov; Nikolay Spiridonov; Eugene V Koonin
Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes.
Molecular biology and evolution 2010;27(8):1745-9.
2010: Eugene V Koonin; Yuri I Wolf
Constraints and plasticity in genome and molecular-phenome evolution.
Nature reviews. Genetics 2010;11(7):487-98.
2010: David M Kristensen; Lavanya Kannan; Michael K Coleman; Yuri I Wolf; Alexander Sorokin; Eugene V Koonin; Arcady Mushegian
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.
Bioinformatics (Oxford, England) 2010;26(12):1481-7.
2010: Elizabeth M Fozo; Kira S Makarova; Svetlana A Shabalina; Natalya Yutin; Eugene V Koonin; Gisela Storz
Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families.
Nucleic acids research 2010;38(11):3743-59.
2010: Eugene V Koonin
Preview. The incredible expanding ancestor of eukaryotes.
Cell 2010;140(5):606-8.
2010: Eugene V Koonin; Bernard Moss
Viruses know more than one way to don a cap.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(8):3283-4.
2010: Alexander E Lobkovsky; Yuri I Wolf; Eugene V Koonin
Universal distribution of protein evolution rates as a consequence of protein folding physics.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(7):2983-8.
2010: Eugene V Koonin; Yuri I Wolf
The common ancestry of life.
Biology direct 2010;5():64.
2010: Kira S Makarova; Eugene V Koonin
Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis.
Archaea (Vancouver, B.C.) 2010;2010():.
2010: Pere Puigbò; Yuri I Wolf; Eugene V Koonin
The tree and net components of prokaryote evolution.
Genome biology and evolution 2010;2():745-56.
2010: Svetlana A Shabalina; Alexey N Spiridonov; Nikolay Spiridonov; Eugene V Koonin
Connections between alternative transcription and alternative splicing in mammals.
Genome biology and evolution 2010;2():791-9.
2010: Yuri I Wolf; Irina V Gopich; David Lipman; Eugene V Koonin
Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes.
Genome biology and evolution 2010;2():190-9.
2010: Eugene V Koonin; Natalya Yutin
Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses.
Intervirology 2010;53(5):284-92.
2010: Jiri Pavlicek; Sandrine Sauzet; Laurence Besseau; Steven L Coon; joan weller; Gilles Boeuf; Pascaline Gaildrat; Marina V Omelchenko; Eugene V Koonin; Jack Falcón; David Klein
Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus.
BMC evolutionary biology 2010;10():154.
2010: 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.
Advances in bioinformatics 2010;():167408.
2010: Kira S Makarova; Eugene V Koonin
Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.
Biology direct 2010;5():33.
2010: Eugene V Koonin
The origin and early evolution of eukaryotes in the light of phylogenomics.
Genome biology 2010;11(5):209.
2010: Marina V Omelchenko; Michael Galperin; Yuri I Wolf; Eugene V Koonin
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.
Biology direct 2010;5():31.
2010: Eugene V Koonin
Taming of the shrewd: novel eukaryotic genes from RNA viruses.
BMC biology 2010;8():2.
2010: David M Kristensen; Arcady R Mushegian; Valerian V Dolja; Eugene V Koonin
New dimensions of the virus world discovered through metagenomics.
Trends in microbiology 2010;18(1):11-9.
2009: Mickael Boyer; Natalya Yutin; Isabelle Pagnier; Lina Barrassi; Ghislain Fournous; Leon Espinosa; Catherine Robert; Saïd Azza; Siyang Sun; Michael G Rossmann; Marie Suzan-Monti; Bernard La Scola; Eugene V Koonin; Didier Raoult
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(51):21848-53.
2009: Eugene V Koonin
The Origin at 150: is a new evolutionary synthesis in sight?
Trends in genetics : TIG 2009;25(11):473-5.
2009: Manuel Irimia; Scott William Roy; Daniel E Neafsey; Josep F Abril; Jordi Garcia-Fernandez; Eugene V Koonin
Complex selection on 5' splice sites in intron-rich organisms.
Genome research 2009;19(11):2021-7.
2009: Yang Huang; Eugene V Koonin; David Lipman; Teresa M Przytycka
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.
Nucleic acids research 2009;37(20):6799-810.
2009: Tatiana G Senkevich; Eugene V Koonin; Bernard Moss
Predicted poxvirus FEN1-like nuclease required for homologous recombination, double-strand break repair and full-size genome formation.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(42):17921-6.
2009: Eugene V Koonin
On the origin of cells and viruses: primordial virus world scenario.
Annals of the New York Academy of Sciences 2009;1178():47-64.
2009: Itai Sharon; Ariella Alperovitch; Forest Rohwer; Matthew Haynes; Fabian Glaser; Nof Atamna-Ismaeel; Ron Y Pinter; Frédéric Partensky; Eugene V Koonin; Yuri I Wolf; Nathan Nelson; Oded Béjà
Photosystem I gene cassettes are present in marine virus genomes.
Nature 2009;461(7261):258-62.
2009: Eugene V Koonin
Intron-dominated genomes of early ancestors of eukaryotes.
The Journal of heredity 2009;100(5):618-23.
2009: Eugene V Koonin; Tatiana G Senkevich; Valerian V Dolja
Compelling reasons why viruses are relevant for the origin of cells.
Nature reviews. Microbiology 2009;7(8):615; author reply 615.
2009: Eugene V Koonin; L Aravind
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.
Cell cycle (Georgetown, Tex.) 2009;8(13):1984-5.
2009: Yuri I Wolf; Pavel Novichkov; Georgy P Karev; Eugene V Koonin; David Lipman
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(18):7273-80.
2009: Armen Y Mulkidjanian; Michael Galperin; Eugene V Koonin
Co-evolution of primordial membranes and membrane proteins.
Trends in biochemical sciences 2009;34(4):206-15.
2009: Eugene V Koonin
Towards a postmodern synthesis of evolutionary biology.
Cell cycle (Georgetown, Tex.) 2009;8(6):799-800.
2009: Eugene V Koonin
Darwinian evolution in the light of genomics.
Nucleic acids research 2009;37(4):1011-34.
2009: Eugene V Koonin; Artem S Novozhilov
Origin and evolution of the genetic code: the universal enigma.
IUBMB life 2009;61(2):99-111.
2009: Eugene V Koonin
Evolution of genome architecture.
The international journal of biochemistry & cell biology 2009;41(2):298-306.
2009: Liran Carmel; Eugene V Koonin
A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes.
Genome biology and evolution 2009;1():382-90.
2009: Igor B Rogozin; Malay Kumar Basu; Miklós Csürös; Eugene V Koonin
Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes.
Genome biology and evolution 2009;1():99-113.
2009: Natalya Yutin; Eugene V Koonin
Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity.
Biology direct 2009;4():51.
2009: Natalya Yutin; Yuri I Wolf; Didier Raoult; Eugene V Koonin
Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution.
Virology journal 2009;6():223.
2009: Artem S Novozhilov; Eugene V Koonin
Exceptional error minimization in putative primordial genetic codes.
Biology direct 2009;4():44.
2009: Eugene V Koonin; Yuri I Wolf
Is evolution Darwinian or/and Lamarckian?
Biology direct 2009;4():42.
2009: Fabian Blombach; Kira S Makarova; Jeannette Marrero; Bettina Siebers; Eugene V Koonin; John van der Oost
Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea.
Biology direct 2009;4():39.
2009: Eugene V Koonin; Yuri I Wolf
The fundamental units, processes and patterns of evolution, and the tree of life conundrum.
Biology direct 2009;4():33.
2009: Kira S Makarova; Yuri I Wolf; John van der Oost; Eugene V Koonin
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.
Biology direct 2009;4():29.
2009: Eugene V Koonin; Yuri I Wolf; Pere Puigbò
The phylogenetic forest and the quest for the elusive tree of life.
Cold Spring Harbor symposia on quantitative biology 2009;74():205-13.
2009: Pere Puigbò; Yuri I Wolf; Eugene V Koonin
Search for a 'Tree of Life' in the thicket of the phylogenetic forest.
Journal of biology 2009;8(6):59.
2009: Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.
Biology direct 2009;4():19.
2009: C Leong Ng; David G Waterman; Eugene V Koonin; Alison D Walters; James P J Chong; Michail N Isupov; Andrey A Lebedev; David H J Bunka; Peter G Stockley; Miguel Ortiz-Lombardía; Alfred A Antson
Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein.
BMC structural biology 2009;9():32.
2009: Liran Carmel; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure.
Methods in molecular biology (Clifton, N.J.) 2009;541():357-71.
2009: Alissa M Resch; Aleksey Y Ogurtsov; Igor Rogozin; Svetlana A Shabalina; Eugene V Koonin
Evolution of alternative and constitutive regions of mammalian 5'UTRs.
BMC genomics 2009;10():162.
2009: Tahir Tahirov; Kira S Makarova; Igor Rogozin; Youri I Pavlov; Eugene V Koonin
Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors.
Biology direct 2009;4():11.
2009: Natalya Yutin; Maxim Y Wolf; Yuri I Wolf; Eugene V Koonin
The origins of phagocytosis and eukaryogenesis.
Biology direct 2009;4():9.
2008: Eugene V Koonin; Yuri I Wolf; Keizo Nagasaki; Valerian V Dolja
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.
Nature reviews. Microbiology 2008;6(12):925-39.
2008: Eugene V Koonin; Yuri I Wolf
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.
Nucleic acids research 2008;36(21):6688-719.
2008: Malay Kumar Basu; Igor Rogozin; Eugene V Koonin
Primordial spliceosomal introns were probably U2-type.
Trends in genetics : TIG 2008;24(11):525-8.
2008: Andrey G Baranovskiy; Nigar D Babayeva; Victoria G Liston; Igor Rogozin; Eugene V Koonin; Youri I Pavlov; Dmitry G Vassylyev; Tahir Tahirov
X-ray structure of the complex of regulatory subunits of human DNA polymerase delta.
Cell cycle (Georgetown, Tex.) 2008;7(19):3026-36.
2008: Raquel Assis; Alexey S Kondrashov; Eugene V Koonin; Fyodor A Kondrashov
Nested genes and increasing organizational complexity of metazoan genomes.
Trends in genetics : TIG 2008;24(10):475-8.
2008: Erwin van den Born; Marina V Omelchenko; Anders Bekkelund; Vibeke Leihne; Eugene V Koonin; Valerian V Dolja; Pål Ø Falnes
Viral AlkB proteins repair RNA damage by oxidative demethylation.
Nucleic acids research 2008;36(17):5451-61.
2008: Svetlana A Shabalina; Eugene V Koonin
Origins and evolution of eukaryotic RNA interference.
Trends in ecology & evolution 2008;23(10):578-87.
2008: Stan J J Brouns; Matthijs M Jore; Magnus Lundgren; Edze R Westra; Rik J H Slijkhuis; Ambrosius Snijders; Mark J Dickman; Kira S Makarova; Eugene V Koonin; John van der Oost
Small CRISPR RNAs guide antiviral defense in prokaryotes.
Science (New York, N.Y.) 2008;321(5891):960-4.
2008: Natalya Yutin; Kira S Makarova; Sergei L Mekhedov; Yuri I Wolf; Eugene V Koonin
The deep archaeal roots of eukaryotes.
Molecular biology and evolution 2008;25(8):1619-30.
2008: Natalia Beloglazova; Greg Brown; Matthew D Zimmerman; Michael Proudfoot; Kira S Makarova; Marina Kudritska; Samvel Kochinyan; Shuren Wang; Maksymilian Chruszcz; Wladek Minor; Eugene V Koonin; Aled M Edwards; Alexei Savchenko; Alexander F Yakunin
A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.
The Journal of biological chemistry 2008;283(29):20361-71.
2008: James G Elkins; Mircea Podar; David E Graham; Kira S Makarova; Yuri Wolf; Lennart Randau; Brian P Hedlund; Céline Brochier-Armanet; Victor Kunin; Iain Anderson; Alla Lapidus; Eugene Goltsman; Kerrie Barry; Eugene V Koonin; Phil Hugenholtz; Nikos Kyrpides; Gerhard Wanner; Paul Richardson; Martin Keller; Karl O Stetter
A korarchaeal genome reveals insights into the evolution of the Archaea.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(23):8102-7.
2008: Tatiana G Senkevich; Linda S Wyatt; Andrea S Weisberg; Eugene V Koonin; Bernard Moss
A conserved poxvirus NlpC/P60 superfamily protein contributes to vaccinia virus virulence in mice but not to replication in cell culture.
Virology 2008;374(2):506-14.
2008: Miklós Csurös; Igor Rogozin; Eugene V Koonin
Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach.
Molecular biology and evolution 2008;25(5):903-11.
2008: J Nicole Kosarek; Rachel V Woodruff; Amanda Rivera-Begeman; Caixia Guo; Sanjay D'Souza; Eugene V Koonin; Graham C Walker; Errol C Friedberg
Comparative analysis of in vivo interactions between Rev1 protein and other Y-family DNA polymerases in animals and yeasts.
DNA repair 2008;7(3):439-51.
2008: Malay Kumar Basu; Liran Carmel; Igor Rogozin; Eugene V Koonin
Evolution of protein domain promiscuity in eukaryotes.
Genome research 2008;18(3):449-61.
2008: Dror Avisar; Alexey I Prokhnevsky; Kira S Makarova; Eugene V Koonin; Valerian V Dolja
Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana.
Plant physiology 2008;146(3):1098-108.
2008: Jimmy Saw; Bruce W Mountain; Lu Feng; Marina V Omelchenko; Shaobin Hou; Jennifer A Saito; Matthew B Stott; Dan Li; Guang Zhao; Junli Wu; Michael Galperin; Eugene V Koonin; Kira S Makarova; Yuri I Wolf; Daniel J Rigden; Peter F Dunfield; Lei Wang; Maqsudul Alam
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1.
Genome biology 2008;9(11):R161.
2008: Mircea Podar; Iain Anderson; Kira S Makarova; James G Elkins; Natalia Ivanova; Mark A Wall; Athanasios Lykidis; Kostantinos Mavromatis; Hui Sun; Matthew Hudson; Wenqiong Chen; Cosmin Deciu; Don Hutchison; Jonathan R Eads; Abraham Anderson; Fillipe Fernandes; Ernest Szeto; Alla Lapidus; Nikos Kyrpides; Milton H Saier; Paul M Richardson; Reinhard Rachel; Harald Huber; Jonathan Eisen; Eugene V Koonin; Martin Keller; Karl O Stetter
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.
Genome biology 2008;9(11):R158.
2008: Maxim Y Wolf; Yuri I Wolf; Eugene V Koonin
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution.
Biology direct 2008;3():40.
2008: Igor Rogozin; Kira S Makarova; Youri I Pavlov; Eugene V Koonin
A highly conserved family of inactivated archaeal B family DNA polymerases.
Biology direct 2008;3():32.
2008: Alexander Churbanov; Stephen Winters-Hilt; Eugene V Koonin; Igor Rogozin
Accumulation of GC donor splice signals in mammals.
Biology direct 2008;3():30.
2008: Shaobin Hou; Kira S Makarova; Jimmy Saw; Pavel Senin; Benjamin V Ly; Zhemin Zhou; Yan Ren; Jianmei Wang; Michael Galperin; Marina V Omelchenko; Yuri I Wolf; Natalya Yutin; Eugene V Koonin; Matthew B Stott; Bruce W Mountain; Michelle A Crowe; Angela Smirnova; Peter F Dunfield; Lu Feng; Lei Wang; Maqsudul Alam
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.
Biology direct 2008;3():26.
2008: Malay Kumar Basu; Wojciech Makalowski; Igor Rogozin; Eugene V Koonin
U12 intron positions are more strongly conserved between animals and plants than U2 intron positions.
Biology direct 2008;3():19.
2008: Armen Y Mulkidjanian; Michael Galperin; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Evolutionary primacy of sodium bioenergetics.
Biology direct 2008;3():13.
2008: Igor Rogozin; Karen Thomson; Miklós Csürös; Liran Carmel; Eugene V Koonin
Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series.
Biology direct 2008;3():7.
2008: Mircea Podar; Mark A Wall; Kira S Makarova; Eugene V Koonin
The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system.
Biology direct 2008;3():2.
2008: Malay Kumar Basu; Igor Rogozin; Oliver Deusch; Tal Dagan; William Martin; Eugene V Koonin
Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues.
Molecular biology and evolution 2008;25(1):111-9.
2007: Igor Rogozin; Yuri I Wolf; Liran Carmel; Eugene V Koonin
Analysis of rare amino acid replacements supports the Coelomata clade.
Molecular biology and evolution 2007;24(12):2594-7.
2007: Frank S De Silva; Whitney Lewis; Peter Berglund; Eugene V Koonin; Bernard Moss
Poxvirus DNA primase.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(47):18724-9.
2007: Armen Y Mulkidjanian; Kira S Makarova; Michael Galperin; Eugene V Koonin
Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.
Nature reviews. Microbiology 2007;5(11):892-9.
2007: Jie Zheng; Igor Rogozin; Eugene V Koonin; Teresa M Przytycka
Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation.
Molecular biology and evolution 2007;24(11):2583-92.
2007: Maria V Vitushkina; Igor Rogozin; Wilhelm Jelkmann; Eugene V Koonin; Alexey A Agranovsky
Completion of the mapping of transcription start sites for the five-gene block subgenomic RNAs of Beet yellows Closterovirus and identification of putative subgenomic promoters.
Virus research 2007;128(1-2):153-8.
2007: Alissa M Resch; Liran Carmel; Leonardo Mariño-Ramírez; Aleksey Y Ogurtsov; Svetlana A Shabalina; Igor Rogozin; Eugene V Koonin
Widespread positive selection in synonymous sites of mammalian genes.
Molecular biology and evolution 2007;24(8):1821-31.
2007: Liran Carmel; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
Evolutionarily conserved genes preferentially accumulate introns.
Genome research 2007;17(7):1045-50.
2007: Liran Carmel; Yuri I Wolf; Igor Rogozin; Eugene V Koonin
Three distinct modes of intron dynamics in the evolution of eukaryotes.
Genome research 2007;17(7):1034-44.
2007: Eugene V Koonin
An RNA-making reactor for the origin of life.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(22):9105-6.
2007: Eugene V Koonin
Metagenomic sorcery and the expanding protein universe.
Nature biotechnology 2007;25(5):540-2.
2007: William Martin; Tal Dagan; Eugene V Koonin; Jonathan L Dipippo; J Peter Gogarten; James A Lake
The evolution of eukaryotes.
Science (New York, N.Y.) 2007;316(5824):542-3; author reply 542-3.
2007: Igor Rogozin; Yuri I Wolf; Liran Carmel; Eugene V Koonin
Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements.
Molecular biology and evolution 2007;24(4):1080-90.
2007: Alexander V Sverdlov; Miklos Csuros; Igor Rogozin; Eugene V Koonin
A glimpse of a putative pre-intron phase of eukaryotic evolution.
Trends in genetics : TIG 2007;23(3):105-8.
2007: Kira S Makarova; Eugene V Koonin
Evolutionary genomics of lactic acid bacteria.
Journal of bacteriology 2007;189(4):1199-208.
2007: Eugene V Koonin; Kira S Makarova; James G Elkins
Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".
Biology direct 2007;2():38.
2007: Kira S Makarova; Alexander V Sorokin; Pavel Novichkov; Yuri I Wolf; Eugene V Koonin
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
Biology direct 2007;2():33.
2007: Artem S Novozhilov; Yuri I Wolf; Eugene V Koonin
Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape.
Biology direct 2007;2():24.
2007: Liran Carmel; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
Patterns of intron gain and conservation in eukaryotic genes.
BMC evolutionary biology 2007;7():192.
2007: Kira S Makarova; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Alla Lapidus; Alex Copeland; Edwin Kim; Miriam Land; Konstantinos Mavrommatis; Samuel Pitluck; Paul M Richardson; Chris Detter; Thomas S Brettin; Elizabeth Saunders; Barry Lai; Bruce Ravel; Kenneth M Kemner; Yuri I Wolf; Alexei Sorokin; Anna V Gerasimova; Mikhail S Gelfand; James K Fredrickson; Eugene V Koonin; Michael J Daly
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
PloS one 2007;2(9):e955.
2007: Eugene V Koonin
The Biological Big Bang model for the major transitions in evolution.
Biology direct 2007;2():21.
2007: Eugene V Koonin
The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life.
Biology direct 2007;2():15.
2007: Yuri I Wolf; Eugene V Koonin
On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization.
Biology direct 2007;2():14.
2007: Eugene V Koonin
Chance and necessity in cellular response to challenge.
Molecular systems biology 2007;3():107.
2006: Borya Shakhnovich; Eugene V Koonin
Origins and impact of constraints in evolution of gene families.
Genome research 2006;16(12):1529-36.
2006: Frederick F Correia; Anthony D'Onofrio; Tomas Rejtar; Lingyun Li; Barry L Karger; Kira Makarova; Eugene V Koonin; Kim Lewis
Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli.
Journal of bacteriology 2006;188(24):8360-7.
2006: Ekaterina Kuznetsova; Michael Proudfoot; Claudio F Gonzalez; Greg Brown; Marina V Omelchenko; Ivan Borozan; Liran Carmel; Yuri I Wolf; Hirotada Mori; Alexei V Savchenko; Cheryl H Arrowsmith; Eugene V Koonin; Aled M Edwards; Alexander F Yakunin
Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family.
The Journal of biological chemistry 2006;281(47):36149-61.
2006: Kira S Makarova; Nick V Grishin; Eugene V Koonin
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinformatics (Oxford, England) 2006;22(21):2581-4.
2006: Eugene V Koonin; Yuri I Wolf
Evolutionary systems biology: links between gene evolution and function.
Current opinion in biotechnology 2006;17(5):481-7.
2006: Armen Y Mulkidjanian; Eugene V Koonin; Kira S Makarova; Sergei L Mekhedov; Alexei Sorokin; Yuri I Wolf; Alexis Dufresne; Frédéric Partensky; Henry Burd; Denis Kaznadzey; Robert Haselkorn; Michael Galperin
The cyanobacterial genome core and the origin of photosynthesis.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(35):13126-31.
2006: William Martin; Eugene V Koonin
A positive definition of prokaryotes.
Nature 2006;442(7105):868.
2006: Yuri I Wolf; Liran Carmel; Eugene V Koonin
Unifying measures of gene function and evolution.
Proceedings. Biological sciences / The Royal Society 2006;273(1593):1507-15.
2006: L Aravind; Lakshminarayan M Iyer; Eugene V Koonin
Comparative genomics and structural biology of the molecular innovations of eukaryotes.
Current opinion in structural biology 2006;16(3):409-19.
2006: Kira S Makarova; Eugene V Koonin; Robert Haselkorn; Michael Galperin
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion.
Bioinformatics (Oxford, England) 2006;22(11):1297-301.
2006: Nina Marinsek; Elizabeth R Barry; Kira S Makarova; Isabelle Dionne; Eugene V Koonin; Steve Bell
GINS, a central nexus in the archaeal DNA replication fork.
EMBO reports 2006;7(5):539-45.
2006: David Prangishvili; Roger A Garrett; Eugene V Koonin
Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life.
Virus research 2006;117(1):52-67.
2006: Eugene V Koonin; Valerian V Dolja
Evolution of complexity in the viral world: the dawn of a new vision.
Virus research 2006;117(1):1-4.
2006: Lakshminarayan M Iyer; S Balaji; Eugene V Koonin; L Aravind
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.
Virus research 2006;117(1):156-84.
2006: William Martin; Eugene V Koonin
Introns and the origin of nucleus-cytosol compartmentalization.
Nature 2006;440(7080):41-5.
2006: Artem S Novozhilov; Georgy P Karev; Eugene V Koonin
Biological applications of the theory of birth-and-death processes.
Briefings in bioinformatics 2006;7(1):70-85.
2006: Marin Chiba; Jonathan C Reed; Alexey I Prokhnevsky; Elisabeth J Chapman; Munir Mawassi; Eugene V Koonin; James C Carrington; Valerian V Dolja
Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon.
Virology 2006;346(1):7-14.
2006: David G Waterman; Miguel Ortiz-Lombardía; Mark J Fogg; Eugene V Koonin; Alfred A Antson
Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain.
Journal of molecular biology 2006;356(1):97-110.
2006: Eugene V Koonin
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases.
Biology direct 2006;1():39.
2006: Colin N Dewey; Igor Rogozin; Eugene V Koonin
Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns.
BMC genomics 2006;7():311.
2006: Yuri I Wolf; Cécile Viboud; Edward C Holmes; Eugene V Koonin; David Lipman
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus.
Biology direct 2006;1():34.
2006: Fyodor A Kondrashov; Eugene V Koonin; Igor G Morgunov; Tatiana V Finogenova; Marie N Kondrashova
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation.
Biology direct 2006;1():31.
2006: Georgy P Karev; Artem S Novozhilov; Eugene V Koonin
Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics.
Biology direct 2006;1():30.
2006: Eugene V Koonin; Tatiana G Senkevich; Valerian V Dolja
The ancient Virus World and evolution of cells.
Biology direct 2006;1():29.
2006: Panayiotis Tsaparas; Leonardo Mariño-Ramírez; Olivier Bodenreider; Eugene V Koonin; I King Jordan
Global similarity and local divergence in human and mouse gene co-expression networks.
BMC evolutionary biology 2006;6():70.
2006: Eugene V Koonin
The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?
Biology direct 2006;1():22.
2006: Jim Leebens-Mack; Todd Vision; Eric Brenner; John E Bowers; Steven Cannon; Mark J Clement; Clifford W Cunningham; Claude W dePamphilis; Rob DeSalle; Jeff J Doyle; Jonathan Eisen; Xun Gu; John Harshman; Robert K Jansen; Elizabeth A Kellogg; Eugene V Koonin; Brent D Mishler; Hervé Philippe; J Chris Pires; Yin-Long Qiu; Seung-Yon Rhee; Kimmen Sjölander; Douglas E Soltis; Pamela S Soltis; Dennis W Stevenson; Kerr Wall; Tandy Warnow; Christian Zmasek
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).
Omics : a journal of integrative biology 2006;10(2):231-7.
2006: Kira S Makarova; Nick V Grishin; Svetlana A Shabalina; Yuri I Wolf; Eugene V Koonin
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action.
Biology direct 2006;1():7.
2006: Eugene V Koonin; Laura F Landweber; David Lipman
A community experiment with fully open and published peer review.
Biology direct 2006;1():1.
2006: Artem S Novozhilov; Faina S Berezovskaya; Eugene V Koonin; Georgy P Karev
Mathematical modeling of tumor therapy with oncolytic viruses: regimes with complete tumor elimination within the framework of deterministic models.
Biology direct 2006;1():6.
2006: Galina V Glazko; Vladimir N Babenko; Eugene V Koonin; Igor Rogozin
Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection.
Biology direct 2006;1():4.
2006: Vladimir N Babenko; Malay Kumar Basu; Fyodor A Kondrashov; Igor Rogozin; Eugene V Koonin
Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis.
BMC cancer 2006;6():36.
2005: Eugene V Koonin; William Martin
On the origin of genomes and cells within inorganic compartments.
Trends in genetics : TIG 2005;21(12):647-54.
2005: Georgy P Karev; Faina S Berezovskaya; Eugene V Koonin
Modeling genome evolution with a diffusion approximation of a birth-and-death process.
Bioinformatics (Oxford, England) 2005;21 Suppl 3():iii12-9.
2005: Kira S Makarova; Eugene V Koonin
Evolutionary and functional genomics of the Archaea.
Current opinion in microbiology 2005;8(5):586-94.
2005: Eugene V Koonin
Paralogs and mutational robustness linked through transcriptional reprogramming.
BioEssays : news and reviews in molecular, cellular and developmental biology 2005;27(9):865-8.
2005: Igor Rogozin; Malay Kumar Basu; I King Jordan; Youri I Pavlov; Eugene V Koonin
APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis.
Cell cycle (Georgetown, Tex.) 2005;4(9):1281-5.
2005: Julia E Kravchenko; Igor Rogozin; Eugene V Koonin; Peter Chumakov
Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin.
Nature 2005;436(7051):735-9.
2005: Artem S Novozhilov; Georgy P Karev; Eugene V Koonin
Mathematical modeling of evolution of horizontally transferred genes.
Molecular biology and evolution 2005;22(8):1721-32.
2005: Malay Kumar Basu; Eugene V Koonin
Evolution of eukaryotic cysteine sulfinic acid reductase, sulfiredoxin (Srx), from bacterial chromosome partitioning protein ParB.
Cell cycle (Georgetown, Tex.) 2005;4(7):947-52.
2005: Igor Rogozin; Alexander V Sverdlov; Vladimir N Babenko; Eugene V Koonin
Analysis of evolution of exon-intron structure of eukaryotic genes.
Briefings in bioinformatics 2005;6(2):118-34.
2005: Eugene V Koonin; Igor Rogozin; Galina V Glazko
p53 gain-of-function: tumor biology and bioinformatics come together.
Cell cycle (Georgetown, Tex.) 2005;4(5):686-8.
2005: Olga V Moroz; Alexey G Murzin; Kira S Makarova; Eugene V Koonin; Keith S Wilson; Michael Galperin
Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions.
Journal of molecular biology 2005;347(2):243-55.
2005: Eugene V Koonin
Virology: Gulliver among the Lilliputians.
Current biology : CB 2005;15(5):R167-9.
2005: I King Jordan; Fyodor A Kondrashov; Ivan A Adzhubei; Yuri I Wolf; Eugene V Koonin; Alexey S Kondrashov; Shamil Sunyaev
A universal trend of amino acid gain and loss in protein evolution.
Nature 2005;433(7026):633-8.
2005: Luke E Ulrich; Eugene V Koonin; Igor B Zhulin
One-component systems dominate signal transduction in prokaryotes.
Trends in microbiology 2005;13(2):52-6.
2005: Galina V Glazko; Eugene V Koonin; Igor Rogozin
Molecular dating: ape bones agree with chicken entrails.
Trends in genetics : TIG 2005;21(2):89-92.
2005: Chyan Leong Ng; David G Waterman; Eugene V Koonin; Alfred A Antson; Miguel Ortiz-Lombardía
Crystal structure of Mil (Mth680): internal duplication and similarity between the Imp4/Brix domain and the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases.
EMBO reports 2005;6(2):140-6.
2005: I King Jordan; Leonardo Mariño-Ramírez; Eugene V Koonin
Evolutionary significance of gene expression divergence.
Gene 2005;345(1):119-26.
2005: Eugene V Koonin
Systemic determinants of gene evolution and function.
Molecular systems biology 2005;1():2005.0021.
2005: Eugene V Koonin
Orthologs, paralogs, and evolutionary genomics.
Annual review of genetics 2005;39():309-38.
2005: Marina V Omelchenko; Yuri I Wolf; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Michael J Daly; Eugene V Koonin; Kira S Makarova
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.
BMC evolutionary biology 2005;5():57.
2005: Alexander Churbanov; Igor Rogozin; Vladimir N Babenko; Hesham Ali; Eugene V Koonin
Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes.
Nucleic acids research 2005;33(17):5512-20.
2005: Kira S Makarova; Yuri I Wolf; Sergei L Mekhedov; Boris G Mirkin; Eugene V Koonin
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.
Nucleic acids research 2005;33(14):4626-38.
2005: Lakshminarayan M Iyer; Eugene V Koonin; Detlef D Leipe; L Aravind
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members.
Nucleic acids research 2005;33(12):3875-96.
2005: Alexander V Sverdlov; Igor Rogozin; Vladimir N Babenko; Eugene V Koonin
Conservation versus parallel gains in intron evolution.
Nucleic acids research 2005;33(6):1741-8.
2004: Shaobin Hou; Jimmy Saw; Kit Shan Lee; Tracey Allen K Freitas; Claude Belisle; Yutaka Kawarabayasi; Stuart P Donachie; Alla Pikina; Michael Galperin; Eugene V Koonin; Kira S Makarova; Marina V Omelchenko; Alexei Sorokin; Yuri I Wolf; Qing X Li; Young-Soo Keum; Sonia Campbell; Judith Denery; Shin-Ichi Aizawa; Satoshi Shibata; Alexander Malahoff; Maqsudul Alam
Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(52):18036-41.
2004: Ben Mans; Vivek Anantharaman; L Aravind; Eugene V Koonin
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.
Cell cycle (Georgetown, Tex.) 2004;3(12):1612-37.
2004: Thijs J G Ettema; Kira S Makarova; Gera L Jellema; Hinco J Gierman; Eugene V Koonin; Martijn A Huynen; WILLEM DE VOS; John van der Oost
Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism.
Journal of bacteriology 2004;186(22):7754-62.
2004: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Novel predicted peptidases with a potential role in the ubiquitin signaling pathway.
Cell cycle (Georgetown, Tex.) 2004;3(11):1440-50.
2004: I King Jordan; Leonardo Mariño-Ramírez; Yuri I Wolf; Eugene V Koonin
Conservation and coevolution in the scale-free human gene coexpression network.
Molecular biology and evolution 2004;21(11):2058-70.
2004: Detlef D Leipe; Eugene V Koonin; L Aravind
STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer.
Journal of molecular biology 2004;343(1):1-28.
2004: Pavel Novichkov; Marina V Omelchenko; Mikhail S Gelfand; Andrey A Mironov; Yuri I Wolf; Eugene V Koonin
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.
Journal of bacteriology 2004;186(19):6575-85.
2004: Georgy P Karev; Yuri I Wolf; Faina S Berezovskaya; Eugene V Koonin
Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models.
BMC evolutionary biology 2004;4():32.
2004: Alexander V Sverdlov; Igor Rogozin; Vladimir N Babenko; Eugene V Koonin
Reconstruction of ancestral protosplice sites.
Current biology : CB 2004;14(16):1505-8.
2004: Alexander V Sverdlov; Vladimir N Babenko; Igor Rogozin; Eugene V Koonin
Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion.
Gene 2004;338(1):85-91.
2004: Galina V Glazko; Eugene V Koonin; Igor Rogozin
Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection.
Biochimica et biophysica acta 2004;1679(2):95-106.
2004: Ingrid E Wertz; Karen M O'Rourke; Honglin Zhou; Michael Eby; L Aravind; Somasekar Seshagiri; Ping Wu; Christian Wiesmann; Rohan Baker; David L Boone; Averil Ma; Eugene V Koonin; Xiaodong Huang
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling.
Nature 2004;430(7000):694-9.
2004: I King Jordan; Yuri I Wolf; Eugene V Koonin
Duplicated genes evolve slower than singletons despite the initial rate increase.
BMC evolutionary biology 2004;4():22.
2004: Lakshminarayan M Iyer; L Aravind; Steven L Coon; David Klein; Eugene V Koonin
Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role?
Trends in genetics : TIG 2004;20(7):292-9.
2004: Fyodor A Kondrashov; Eugene V Koonin
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications.
Trends in genetics : TIG 2004;20(7):287-90.
2004: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer.
Gene 2004;335():73-88.
2004: Igor Rogozin; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes.
Briefings in bioinformatics 2004;5(2):131-49.
2004: Andrei V Budanov; Anna A Sablina; Elena Feinstein; Eugene V Koonin; Peter Chumakov
Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD.
Science (New York, N.Y.) 2004;304(5670):596-600.
2004: Attila Sík; Brent J Passer; Eugene V Koonin; Luca Pellegrini
Self-regulated cleavage of the mitochondrial intramembrane-cleaving protease PARL yields Pbeta, a nuclear-targeted peptide.
The Journal of biological chemistry 2004;279(15):15323-9.
2004: Lakshminarayan M Iyer; Detlef D Leipe; Eugene V Koonin; L Aravind
Evolutionary history and higher order classification of AAA+ ATPases.
Journal of structural biology 2004;146(1-2):11-31.
2004: Natalay Kouprina; Michael Mullokandov; Igor Rogozin; N Keith Collins; Greg Solomon; John Otstot; John Risinger; Eugene V Koonin; J Carl Barrett; Vladimir Larionov
The SPANX gene family of cancer/testis-specific antigens: rapid evolution and amplification in African great apes and hominids.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(9):3077-82.
2004: Eugene V Koonin
A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man.
Cell cycle (Georgetown, Tex.) 2004;3(3):280-5.
2004: Eugene V Koonin
Eugene V. Koonin.
Current biology : CB 2004;14(3):R96-7.
2004: Michael Galperin; Eugene V Koonin
'Conserved hypothetical' proteins: prioritization of targets for experimental study.
Nucleic acids research 2004;32(18):5452-63.
2004: Lakshminarayan M Iyer; Kira S Makarova; Eugene V Koonin; L Aravind
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.
Nucleic acids research 2004;32(17):5260-79.
2004: Vladimir N Babenko; Igor Rogozin; Sergei L Mekhedov; Eugene V Koonin
Prevalence of intron gain over intron loss in the evolution of paralogous gene families.
Nucleic acids research 2004;32(12):3724-33.
2004: L Aravind; Lakshminarayan M Iyer; Detlef D Leipe; Eugene V Koonin
A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain.
Genome biology 2004;5(5):R30.
2004: Svetlana A Shabalina; Aleksey Y Ogurtsov; Igor Rogozin; Eugene V Koonin; David Lipman
Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.
Nucleic acids research 2004;32(5):1774-82.
2004: Eugene V Koonin; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Anastasia N Nikolskaya; B Sridhar Rao; Igor Rogozin; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Genome biology 2004;5(2):R7.
2004: Yuri I Wolf; Igor Rogozin; Eugene V Koonin
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.
Genome research 2004;14(1):29-36.
2003: Alexander V Sverdlov; Igor Rogozin; Vladimir N Babenko; Eugene V Koonin
Evidence of splice signal migration from exon to intron during intron evolution.
Current biology : CB 2003;13(24):2170-4.
2003: Eugene V Koonin
Comparative genomics, minimal gene-sets and the last universal common ancestor.
Nature reviews. Microbiology 2003;1(2):127-36.
2003: Eugene V Koonin
Horizontal gene transfer: the path to maturity.
Molecular microbiology 2003;50(3):725-7.
2003: Detlef D Leipe; Eugene V Koonin; L Aravind
Evolution and classification of P-loop kinases and related proteins.
Journal of molecular biology 2003;333(4):781-815.
2003: Georgy P Karev; Yuri I Wolf; Eugene V Koonin
Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?
Bioinformatics (Oxford, England) 2003;19(15):1889-900.
2003: Kira S Makarova; Eugene V Koonin
Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis.
FEMS microbiology letters 2003;227(1):17-23.
2003: Dmitri M Krylov; Yuri I Wolf; Igor Rogozin; Eugene V Koonin
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.
Genome research 2003;13(10):2229-35.
2003: Roman L Tatusov; Natalie Fedorova Abrams; 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 Yin; Darren A Natale
The COG database: an updated version includes eukaryotes.
BMC bioinformatics 2003;4():41.
2003: Igor Rogozin; Yuri I Wolf; Alexander V Sorokin; Boris G Mirkin; Eugene V Koonin
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution.
Current biology : CB 2003;13(17):1512-7.
2003: Alexis Dufresne; Marcel Salanoubat; Frédéric Partensky; François Artiguenave; Ilka M Axmann; Valérie Barbe; Simone Duprat; Michael Galperin; Eugene V Koonin; Florence Le Gall; Kira S Makarova; Martin Ostrowski; Sophie Oztas; Catherine Robert; Igor Rogozin; David J Scanlan; Nicole Tandeau de Marsac; Jean Weissenbach; Patrick Wincker; Yuri I Wolf; Wolfgang Hess
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(17):10020-5.
2003: Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Potential genomic determinants of hyperthermophily.
Trends in genetics : TIG 2003;19(4):172-6.
2003: Yongqing Liu; ali khawwam; Marina V Omelchenko; Alex S Beliaev; Amudhan Venkateswaran; Julia Stair; Liyou Wu; Dorothea K Thompson; Dong Xu; Igor Rogozin; Elena K Gaidamakova; Min Zhai; Kira S Makarova; Eugene V Koonin; Michael J Daly
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(7):4191-6.
2003: Eugene V Koonin
Swift publication would reward good reviewers.
Nature 2003;422(6930):374.
2003: Igor Rogozin; L Aravind; Eugene V Koonin
Differential action of natural selection on the N and C-terminal domains of 2'-5' oligoadenylate synthetases and the potential nuclease function of the C-terminal domain.
Journal of molecular biology 2003;326(5):1449-61.
2003: L Aravind; Lakshminarayan M Iyer; Eugene V Koonin
Scores of RINGS but no PHDs in ubiquitin signaling.
Cell cycle (Georgetown, Tex.) 2003;2(2):123-6.
2003: Wei Yang; Igor Rogozin; Eugene V Koonin
Yeast POL5 is an evolutionarily conserved regulator of rDNA transcription unrelated to any known DNA polymerases.
Cell cycle (Georgetown, Tex.) 2003;2(2):120-2.
2003: Galina V Glazko; Eugene V Koonin; Igor Rogozin; Svetlana A Shabalina
A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions.
Trends in genetics : TIG 2003;19(3):119-24.
2003: Fyodor A Kondrashov; Eugene V Koonin
Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences.
Trends in genetics : TIG 2003;19(3):115-9.
2003: Alberto J Napuli; Dina V Alzhanova; Catalin E Doneanu; Douglas F Barofsky; Eugene V Koonin; Valerian V Dolja
The 64-kilodalton capsid protein homolog of Beet yellows virus is required for assembly of virion tails.
Journal of virology 2003;77(4):2377-84.
2003: I King Jordan; Igor Rogozin; Galina V Glazko; Eugene V Koonin
Origin of a substantial fraction of human regulatory sequences from transposable elements.
Trends in genetics : TIG 2003;19(2):68-72.
2003: Vivek Anantharaman; L Aravind; Eugene V Koonin
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins.
Current opinion in chemical biology 2003;7(1):12-20.
2003: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases.
BMC structural biology 2003;3():1.
2003: Dmitri M Krylov; Kim Nasmyth; Eugene V Koonin
Evolution of eukaryotic cell cycle regulation: stepwise addition of regulatory kinases and late advent of the CDKs.
Current biology : CB 2003;13(2):173-7.
2003: I King Jordan; Yuri I Wolf; Eugene V Koonin
No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly.
BMC evolutionary biology 2003;3():1.
2003: Boris G Mirkin; Trevor I Fenner; Michael Galperin; Eugene V Koonin
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.
BMC evolutionary biology 2003;3():2.
2003: Igor Rogozin; Vladimir N Babenko; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Boris G Mirkin; Anastasia N Nikolskaya; B Sridhar Rao; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale; Eugene V Koonin
Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.
Cold Spring Harbor symposia on quantitative biology 2003;68():293-301.
2003: Marina V Omelchenko; Kira S Makarova; Yuri I Wolf; Igor Rogozin; Eugene V Koonin
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.
Genome biology 2003;4(9):R55.
2003: Eugene V Koonin; Igor Rogozin
Getting positive about selection.
Genome biology 2003;4(8):331.
2003: Kira S Makarova; Eugene V Koonin
Comparative genomics of Archaea: how much have we learned in six years, and what's next?
Genome biology 2003;4(8):115.
2003: Vladimir A Ponomarev; Kira S Makarova; L Aravind; Eugene V Koonin
Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb.
Journal of molecular microbiology and biotechnology 2003;5(4):225-9.
2003: I King Jordan; Katrin Henze; Natalie Fedorova Abrams; Eugene V Koonin; Michael Galperin
Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes.
Journal of molecular microbiology and biotechnology 2003;5(3):172-89.
2003: Eugene V Koonin; Kira S Makarova; Igor Rogozin; Laetitia Davidovic; Marie-Claude Letellier; Luca Pellegrini
The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.
Genome biology 2003;4(3):R19.
2002: Erik L L Sonnhammer; Eugene V Koonin
Orthology, paralogy and proposed classification for paralog subtypes.
Trends in genetics : TIG 2002;18(12):619-20.
2002: Eugene V Koonin; Yuri I Wolf; Georgy P Karev
The structure of the protein universe and genome evolution.
Nature 2002;420(6912):218-23.
2002: David Lipman; Alexander Souvorov; Eugene V Koonin; Anna R Panchenko; Tatiana Tatusova
The relationship of protein conservation and sequence length.
BMC evolutionary biology 2002;2():20.
2002: Gregory A Cope; Greg S B Suh; L Aravind; Sylvia E Schwarz; S Lawrence Zipursky; Eugene V Koonin; Raymond J Deshaies
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1.
Science (New York, N.Y.) 2002;298(5593):608-11.
2002: Rati Verma; L Aravind; Robert Oania; W Hayes McDonald; John R Yates; Eugene V Koonin; Raymond J Deshaies
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome.
Science (New York, N.Y.) 2002;298(5593):611-5.
2002: Igor Rogozin; Kira S Makarova; Darren A Natale; Alexey N Spiridonov; Roman L Tatusov; Yuri I Wolf; Jodie Yin; Eugene V Koonin
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.
Nucleic acids research 2002;30(19):4264-71.
2002: Denis M Daigle; Laura Rossi; Albert Berghuis; L Aravind; Eugene V Koonin; Eric D Brown
YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics.
Biochemistry 2002;41(37):11109-17.
2002: Tatiana G Senkevich; Christine L White; Andrea S Weisberg; Joshua A Granek; Elizabeth J Wolffe; Eugene V Koonin; Bernard Moss
Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis.
Virology 2002;300(2):296-303.
2002: Yuri I Wolf; Igor Rogozin; Nick V Grishin; Eugene V Koonin
Genome trees and the tree of life.
Trends in genetics : TIG 2002;18(9):472-9.
2002: Kira S Makarova; L Aravind; Eugene V Koonin
SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes.
Trends in biochemical sciences 2002;27(8):384-6.
2002: Cristian I Castillo-Davis; Sergei L Mekhedov; Daniel L Hartl; Eugene V Koonin; Fyodor A Kondrashov
Selection for short introns in highly expressed genes.
Nature genetics 2002;31(4):415-8.
2002: Olivier Lespinet; Yuri I Wolf; Eugene V Koonin; L Aravind
The role of lineage-specific gene family expansion in the evolution of eukaryotes.
Genome research 2002;12(7):1048-59.
2002: L Aravind; Vivek Anantharaman; Eugene V Koonin
Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.
Proteins 2002;48(1):1-14.
2002: I King Jordan; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
Microevolutionary genomics of bacteria.
Theoretical population biology 2002;61(4):435-47.
2002: L Aravind; Raja Mazumder; Sona Vasudevan; Eugene V Koonin
Trends in protein evolution inferred from sequence and structure analysis.
Current opinion in structural biology 2002;12(3):392-9.
2002: I King Jordan; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria.
Genome research 2002;12(6):962-8.
2002: Igor Rogozin; Kira S Makarova; Janos Murvai; Eva Czabarka; Yuri I Wolf; Roman L Tatusov; Laszlo A Szekely; Eugene V Koonin
Connected gene neighborhoods in prokaryotic genomes.
Nucleic acids research 2002;30(10):2212-23.
2002: Tatiana G Senkevich; Christine L White; Eugene V Koonin; Bernard Moss
Complete pathway for protein disulfide bond formation encoded by poxviruses.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(10):6667-72.
2002: Igor Rogozin; Alexey N Spiridonov; Alexander V Sorokin; Yuri I Wolf; I King Jordan; Roman L Tatusov; Eugene V Koonin
Purifying and directional selection in overlapping prokaryotic genes.
Trends in genetics : TIG 2002;18(5):228-32.
2002: Marina V Omelchenko; Kira S Makarova; Eugene V Koonin
Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain.
FEMS microbiology letters 2002;209(2):255-60.
2002: Alexei I Slesarev; Katja V Mezhevaya; Kira S Makarova; Nikolai Polushin; Olga V Shcherbinina; Vera V Shakhova; Galina I Belova; L Aravind; Darren A Natale; Igor Rogozin; Roman L Tatusov; Yuri I Wolf; Karl O Stetter; Andrei Malykh; Eugene V Koonin; Sergei A Kozyavkin
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4644-9.
2002: Eugene V Koonin; L Aravind
Origin and evolution of eukaryotic apoptosis: the bacterial connection.
Cell death and differentiation 2002;9(4):394-404.
2002: Vivek Anantharaman; Eugene V Koonin; L Aravind
Comparative genomics and evolution of proteins involved in RNA metabolism.
Nucleic acids research 2002;30(7):1427-64.
2002: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52.
BMC genomics 2002;3():8.
2002: Detlef D Leipe; Yuri I Wolf; Eugene V Koonin; L Aravind
Classification and evolution of P-loop GTPases and related ATPases.
Journal of molecular biology 2002;317(1):41-72.
2002: L Aravind; Eugene V Koonin
Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins.
Proteins 2002;46(4):355-67.
2002: Yuri I Wolf; Georgy P Karev; Eugene V Koonin
Scale-free networks in biology: new insights into the fundamentals of evolution?
BioEssays : news and reviews in molecular, cellular and developmental biology 2002;24(2):105-9.
2002: Kira S Makarova; L Aravind; Nick V Grishin; Igor Rogozin; Eugene V Koonin
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
Nucleic acids research 2002;30(2):482-96.
2002: Georgy P Karev; Yuri I Wolf; Andrey Rzhetsky; Faina S Berezovskaya; Eugene V Koonin
Birth and death of protein domains: a simple model of evolution explains power law behavior.
BMC evolutionary biology 2002;2():18.
2002: Itai Yanai; Yuri I Wolf; Eugene V Koonin
Evolution of gene fusions: horizontal transfer versus independent events.
Genome biology 2002;3(5):research0024.
2002: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.
Genome biology 2002;3(3):RESEARCH0012.
2002: Fyodor A Kondrashov; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
Selection in the evolution of gene duplications.
Genome biology 2002;3(2):RESEARCH0008.
2002: Oded Béjà; Eugene V Koonin; L Aravind; Lance Trent Taylor; Heidi Seitz; Jefferey L Stein; Daniel C Bensen; Robert Feldman; Ron Swanson; Edward F DeLong
Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.
Applied and environmental microbiology 2002;68(1):335-45.
2002: Vivek Anantharaman; Eugene V Koonin; L Aravind
SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.
Journal of molecular microbiology and biotechnology 2002;4(1):71-5.
2001: Lakshminarayan M Iyer; L Aravind; Eugene V Koonin
Common origin of four diverse families of large eukaryotic DNA viruses.
Journal of virology 2001;75(23):11720-34.
2001: Fyodor A Kondrashov; Eugene V Koonin
Origin of alternative splicing by tandem exon duplication.
Human molecular genetics 2001;10(23):2661-9.
2001: S N Avedisov; Igor Rogozin; Eugene V Koonin; B J Thomas
Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila.
Molecular biology and evolution 2001;18(11):2110-8.
2001: Yuri I Wolf; Igor Rogozin; Nick V Grishin; Roman L Tatusov; Eugene V Koonin
Genome trees constructed using five different approaches suggest new major bacterial clades.
BMC evolutionary biology 2001;1():8.
2001: Igor Rogozin; Alex 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.
Bioinformatics (Oxford, England) 2001;17(10):890-900.
2001: Michael Galperin; Anastasia N Nikolskaya; Eugene V Koonin
Novel domains of the prokaryotic two-component signal transduction systems.
FEMS microbiology letters 2001;203(1):11-21.
2001: Yuri I Wolf; Fyodor A Kondrashov; Eugene V Koonin
Footprints of primordial introns on the eukaryotic genome: still no clear traces.
Trends in genetics : TIG 2001;17(9):499-501.
2001: Dmitri M Krylov; Eugene V Koonin
A novel family of predicted retroviral-like aspartyl proteases with a possible key role in eukaryotic cell cycle control.
Current biology : CB 2001;11(15):R584-7.
2001: V Anantharaman; Eugene V Koonin; L Aravind
Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold.
Human molecular genetics 2001;10(16):1627-30.
2001: Yuri I Wolf; Eugene V Koonin
Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group.
Trends in genetics : TIG 2001;17(8):431-3.
2001: L Aravind; Eugene V Koonin
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system.
Genome research 2001;11(8):1365-74.
2001: J Nölling; G Breton; Marina V Omelchenko; Kira S Makarova; Qiandong Zeng; R Gibson; H M Lee; J Dubois; D Qiu; J Hitti; Yuri I Wolf; Roman L Tatusov; F Sabathe; Lynn Doucette-Stamm; P Soucaille; Michael J Daly; george bennett; Eugene V Koonin; D R Smith
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.
Journal of bacteriology 2001;183(16):4823-38.
2001: Tatyana N Erokhina; Maria V Vitushkina; Roman A Zinovkin; Dietrich-E Lesemann; Wilhelm Jelkmann; Eugene V Koonin; Alexey A Agranovsky
Ultrastructural localization and epitope mapping of the methyltransferase-like and helicase-like proteins of Beet yellows virus.
The Journal of general virology 2001;82(Pt 8):1983-94.
2001: Alejandro A Schäffer; L Aravind; Thomas L Madden; S Shavirin; John L Spouge; Yuri I Wolf; Eugene V Koonin; Stephen F Altschul
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
Nucleic acids research 2001;29(14):2994-3005.
2001: K R Sreekumar; L Aravind; Eugene V Koonin
Computational analysis of human disease-associated genes and their protein products.
Current opinion in genetics & development 2001;11(3):247-57.
2001: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily.
Proteins 2001;43(2):134-44.
2001: Vivek Anantharaman; Eugene V Koonin; L Aravind
TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes.
FEMS microbiology letters 2001;197(2):215-21.
2001: Vivek Anantharaman; Eugene V Koonin; L Aravind
Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.
Journal of molecular biology 2001;307(5):1271-92.
2001: L Aravind; Eugene V Koonin
THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases.
Trends in biochemical sciences 2001;26(4):215-7.
2001: I King Jordan; Kira S Makarova; John L Spouge; Yuri I Wolf; Eugene V Koonin
Lineage-specific gene expansions in bacterial and archaeal genomes.
Genome research 2001;11(4):555-65.
2001: Eugene V Koonin
Computational genomics.
Current biology : CB 2001;11(5):R155-8.
2001: Kira S Makarova; L Aravind; Yuri I Wolf; Roman L Tatusov; KW Minton; Eugene V Koonin; Michael J Daly
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.
Microbiology and molecular biology reviews : MMBR 2001;65(1):44-79.
2001: Yuri I Wolf; Igor Rogozin; Alexey S Kondrashov; Eugene V Koonin
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
Genome research 2001;11(3):356-72.
2001: L Aravind; V M Dixit; Eugene V Koonin
Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons.
Science (New York, N.Y.) 2001;291(5507):1279-84.
2001: Eugene V Koonin; Yuri I Wolf; L Aravind
Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach.
Genome research 2001;11(2):240-52.
2001: I King Jordan; Fyodor A Kondrashov; Igor Rogozin; Roman L Tatusov; Yuri I Wolf; Eugene V Koonin
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
Genome biology 2001;2(12):RESEARCH0053.
2001: Lakshminarayan M Iyer; L Aravind; P Bork; Kay Hofmann; AR Mushegian; I B Zhulin; Eugene V Koonin
Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Genome biology 2001;2(12):RESEARCH0051.
2001: Kira S Makarova; V A Ponomarev; Eugene V Koonin
Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.
Genome biology 2001;2(9):RESEARCH 0033.
2001: Eugene V Koonin; Kira S Makarova; L Aravind
Horizontal gene transfer in prokaryotes: quantification and classification.
Annual review of microbiology 2001;55():709-42.
2001: Michael Galperin; Eugene V Koonin
Comparative genome analysis.
Methods of biochemical analysis 2001;43():359-92.
2001: Eugene V Koonin
An apology for orthologs - or brave new memes.
Genome biology 2001;2(4):COMMENT1005.
2001: L Aravind; Eugene V Koonin
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases.
Genome biology 2001;2(3):RESEARCH0007.
2001: I King Jordan; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae.
Trends in genetics : TIG 2001;17(1):7-10.
2001: Roman L Tatusov; Darren A Natale; I V Garkavtsev; Tatiana Tatusova; Uma Shankavaram; B Sridhar Rao; Boris Kiryutin; Michael Galperin; Natalie Fedorova Abrams; Eugene V Koonin
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Nucleic acids research 2001;29(1):22-8.
2000: Eugene V Koonin; L Aravind
Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation.
Current biology : CB 2000;10(21):R774-6.
2000: Tatiana G Senkevich; Christine L White; Eugene V Koonin; Bernard Moss
A viral member of the ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(22):12068-73.
2000: L Aravind; H Watanabe; David Lipman; Eugene V Koonin
Lineage-specific loss and divergence of functionally linked genes in eukaryotes.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(21):11319-24.
2000: Oded Béjà; Marcelino Suzuki; Eugene V Koonin; L Aravind; AG Hadd; L P Nguyen; R Villacorta; M Amjadi; C Garrigues; S B Jovanovich; Robert Feldman; Edward F DeLong
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.
Environmental microbiology 2000;2(5):516-29.
2000: Eugene V Koonin; Y I Wolf; A S Kondrashov; L Aravind
Bacterial homologs of the small subunit of eukaryotic DNA primase.
Journal of molecular microbiology and biotechnology 2000;2(4):509-12.
2000: Igor Rogozin; James Lyons-Weiler; Eugene V Koonin
Intron sliding in conserved gene families.
Trends in genetics : TIG 2000;16(10):430-2.
2000: Oded Béjà; L Aravind; Eugene V Koonin; Marcelino Suzuki; AG Hadd; L P Nguyen; S B Jovanovich; C M Gates; Robert Feldman; John L Spudich; Elena N Spudich; Edward F DeLong
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.
Science (New York, N.Y.) 2000;289(5486):1902-6.
2000: L Aravind; Kira S Makarova; Eugene V Koonin
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
Nucleic acids research 2000;28(18):3417-32.
2000: L Aravind; Eugene V Koonin
Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system.
Genome research 2000;10(8):1172-84.
2000: Yuri I Wolf; Fyodor A Kondrashov; Eugene V Koonin
No footprints of primordial introns in a eukaryotic genome.
Trends in genetics : TIG 2000;16(8):333-4.
2000: A D Garcia; L Aravind; Eugene V Koonin; Bernard Moss
Bacterial-type DNA holliday junction resolvases in eukaryotic viruses.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(16):8926-31.
2000: Nick V Grishin; Yuri I Wolf; Eugene V Koonin
From complete genomes to measures of substitution rate variability within and between proteins.
Genome research 2000;10(7):991-1000.
2000: Yuri I Wolf; Nick V Grishin; Eugene V Koonin
Estimating the number of protein folds and families from complete genome data.
Journal of molecular biology 2000;299(4):897-905.
2000: Michael Galperin; Eugene V Koonin
Who's your neighbor? New computational approaches for functional genomics.
Nature biotechnology 2000;18(6):609-13.
2000: L Aravind; Eugene V Koonin
SAP - a putative DNA-binding motif involved in chromosomal organization.
Trends in biochemical sciences 2000;25(3):112-4.
2000: Michael Galperin; L Aravind; Eugene V Koonin
Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea.
FEMS microbiology letters 2000;183(2):259-64.
2000: Piotr Berman; Zhaolei Zhang; Y I Wolf; Eugene V Koonin; Webb Miller
Winnowing sequences from a database search.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):293-302.
2000: Kira S Makarova; L Aravind; Eugene V Koonin
A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae.
Trends in biochemical sciences 2000;25(2):50-2.
2000: Eugene V Koonin
How many genes can make a cell: the minimal-gene-set concept.
Annual review of genomics and human genetics 2000;1():99-116.
2000: Yuri I Wolf; Alexey S Kondrashov; Eugene V Koonin
Interkingdom gene fusions.
Genome biology 2000;1(6):RESEARCH0013.
2000: Darren A Natale; Uma Shankavaram; Michael Galperin; Yuri I Wolf; L Aravind; Eugene V Koonin
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
Genome biology 2000;1(5):RESEARCH0009.
2000: L Aravind; Eugene V Koonin
The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates.
Genome biology 2000;1(4):RESEARCH0007.
2000: Darren A Natale; Michael Galperin; Roman L Tatusov; Eugene V Koonin
Using the COG database to improve gene recognition in complete genomes.
Genetica 2000;108(1):9-17.
2000: Kira S Makarova; L Aravind; Michael J Daly; Eugene V Koonin
Specific expansion of protein families in the radioresistant bacterium Deinococcus radiodurans.
Genetica 2000;108(1):25-34.
2000: Eugene V Koonin; Yuri I Wolf; L Aravind
Protein fold recognition using sequence profiles and its application in structural genomics.
Advances in protein chemistry 2000;54():245-75.
2000: Eugene V Koonin
Bridging the gap between sequence and function.
Trends in genetics : TIG 2000;16(1):16.
2000: Detlef D Leipe; L Aravind; Nick V Grishin; Eugene V Koonin
The bacterial replicative helicase DnaB evolved from a RecA duplication.
Genome research 2000;10(1):5-16.
2000: Roman L Tatusov; Michael Galperin; Darren A Natale; Eugene V Koonin
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Nucleic acids research 2000;28(1):33-6.
1999: Alejandro A Schäffer; Yuri I Wolf; C 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.
Bioinformatics (Oxford, England) 1999;15(12):1000-11.
1999: Michael Galperin; Eugene V Koonin
Searching for drug targets in microbial genomes.
Current opinion in biotechnology 1999;10(6):571-8.
1999: L Aravind; Eugene V Koonin
DNA-binding proteins and evolution of transcription regulation in the archaea.
Nucleic acids research 1999;27(23):4658-70.
1999: Michael Galperin; D A Natale; L Aravind; Eugene V Koonin
A specialized version of the HD hydrolase domain implicated in signal transduction.
Journal of molecular microbiology and biotechnology 1999;1(2):303-5.
1999: Eugene V Koonin; L Aravind; Kay Hofmann; J Tschopp; V M Dixit
Apoptosis. Searching for FLASH domains.
Nature 1999;401(6754):662; discussion 662-3.
1999: L Aravind; Eugene V Koonin
G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins.
Trends in biochemical sciences 1999;24(9):342-4.
1999: Detlef D Leipe; L Aravind; Eugene V Koonin
Did DNA replication evolve twice independently?
Nucleic acids research 1999;27(17):3389-401.
1999: Kira S Makarova; L Aravind; Eugene V Koonin
A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases.
Protein science : a publication of the Protein Society 1999;8(8):1714-9.
1999: Yuri I Wolf; L Aravind; Nick V Grishin; Eugene V Koonin
Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.
Genome research 1999;9(8):689-710.
1999: Kira S Makarova; L Aravind; Michael Galperin; Nick V Grishin; Roman L Tatusov; Yuri I Wolf; Eugene V Koonin
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.
Genome research 1999;9(7):608-28.
1999: C P Ponting; L Aravind; J Schultz; P Bork; Eugene V Koonin
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Journal of molecular biology 1999;289(4):729-45.
1999: Yuri I Wolf; L Aravind; Eugene V Koonin
Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange.
Trends in genetics : TIG 1999;15(5):173-5.
1999: L Aravind; Eugene V Koonin
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches.
Journal of molecular biology 1999;287(5):1023-40.
1999: L Aravind; Eugene V Koonin
DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.
Nucleic acids research 1999;27(7):1609-18.
1999: L Aravind; Eugene V Koonin
Novel predicted RNA-binding domains associated with the translation machinery.
Journal of molecular evolution 1999;48(3):291-302.
1999: L Aravind; DR Walker; Eugene V Koonin
Conserved domains in DNA repair proteins and evolution of repair systems.
Nucleic acids research 1999;27(5):1223-42.
1999: L Aravind; V M Dixit; Eugene V Koonin
The domains of death: evolution of the apoptosis machinery.
Trends in biochemical sciences 1999;24(2):47-53.
1999: L Aravind; Eugene V Koonin
Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain.
Journal of molecular biology 1999;285(4):1353-61.
1999: Michael Galperin; Eugene V Koonin
Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes.
Genetica 1999;106(1-2):159-70.
1999: Yuri I Wolf; Steven E Brenner; P A Bash; Eugene V Koonin
Distribution of protein folds in the three superkingdoms of life.
Genome research 1999;9(1):17-26.
1998: L Aravind; Eugene V Koonin
The HD domain defines a new superfamily of metal-dependent phosphohydrolases.
Trends in biochemical sciences 1998;23(12):469-72.
1998: Stephen F Altschul; Eugene V Koonin
Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.
Trends in biochemical sciences 1998;23(11):444-7.
1998: C J Leonard; L Aravind; Eugene V Koonin
Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily.
Genome research 1998;8(10):1038-47.
1998: L Aravind; Detlef D Leipe; Eugene V Koonin
Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Nucleic acids research 1998;26(18):4205-13.
1998: Zhaolei Zhang; Alejandro A Schäffer; Webb Miller; Thomas L Madden; David Lipman; Eugene V Koonin; Stephen F Altschul
Protein sequence similarity searches using patterns as seeds.
Nucleic acids research 1998;26(17):3986-90.
1998: L Aravind; Eugene V Koonin
Phosphoesterase domains associated with DNA polymerases of diverse origins.
Nucleic acids research 1998;26(16):3746-52.
1998: Michael Galperin; Amos Bairoch; Eugene V Koonin
A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases.
Protein science : a publication of the Protein Society 1998;7(8):1829-35.
1998: L Aravind; Eugene V Koonin
The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair.
Trends in biochemical sciences 1998;23(8):284-6.
1998: Michael Galperin; DR Walker; Eugene V Koonin
Analogous enzymes: independent inventions in enzyme evolution.
Genome research 1998;8(8):779-90.
1998: Eugene V Koonin; Roman L Tatusov; Michael Galperin
Beyond complete genomes: from sequence to structure and function.
Current opinion in structural biology 1998;8(3):355-63.
1998: Eugene V Koonin; L Aravind
Genomics: re-evaluation of translation machinery evolution.
Current biology : CB 1998;8(8):R266-9.
1998: L Aravind; Michael Galperin; Eugene V Koonin
The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold.
Trends in biochemical sciences 1998;23(4):127-9.
1998: Michael Galperin; Eugene V Koonin
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.
In silico biology 1998;1(1):55-67.
1998: Eugene V Koonin; AR Mushegian; Valerian V Dolja
Computer analysis of amino acid sequences. The case of plant virus capsid proteins.
Methods in molecular biology (Clifton, N.J.) 1998;81():319-37.
1998: L Aravind; Eugene V Koonin
A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease.
Trends in biochemical sciences 1998;23(1):17-9.
1997: Eugene V Koonin; Michael Galperin
Prokaryotic genomes: the emerging paradigm of genome-based microbiology.
Current opinion in genetics & development 1997;7(6):757-63.
1997: Michael Galperin; Eugene V Koonin
A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity.
Protein science : a publication of the Protein Society 1997;6(12):2639-43.
1997: Roman L Tatusov; Eugene V Koonin; David Lipman
A genomic perspective on protein families.
Science (New York, N.Y.) 1997;278(5338):631-7.
1997: Eugene V Koonin
Genome sequences: genome sequence of a model prokaryote.
Current biology : CB 1997;7(10):R656-9.
1997: Eugene V Koonin; AR Mushegian; Michael Galperin; DR Walker
Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.
Molecular microbiology 1997;25(4):619-37.
1997: Tatiana G Senkevich; Eugene V Koonin; Joachim Bugert; Gholamreza Darai; Bernard Moss
The genome of molluscum contagiosum virus: analysis and comparison with other poxviruses.
Virology 1997;233(1):19-42.
1997: AR Mushegian; D E Bassett; Mark S Boguski; P Bork; Eugene V Koonin
Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(11):5831-6.
1997: Eugene V Koonin
Big time for small genomes.
Genome research 1997;7(5):418-21.
1996: Eugene V Koonin; AR Mushegian
Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics.
Current opinion in genetics & development 1996;6(6):757-62.
1996: AR Mushegian; Eugene V Koonin
Sequence analysis of eukaryotic developmental proteins: ancient and novel domains.
Genetics 1996;144(2):817-28.
1996: AR Mushegian; Eugene V Koonin
A minimal gene set for cellular life derived by comparison of complete bacterial genomes.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(19):10268-73.
1996: Eugene V Koonin
A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins.
Trends in biochemical sciences 1996;21(7):242-3.
1996: Eugene V Koonin
Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases.
Nucleic acids research 1996;24(12):2411-5.
1996: Eugene V Koonin; AR Mushegian; Kenneth E Rudd
Sequencing and analysis of bacterial genomes.
Current biology : CB 1996;6(4):404-16.
1996: Eugene V Koonin; P Bork
Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes.
Trends in biochemical sciences 1996;21(4):128-9.
1996: Roman L Tatusov; AR Mushegian; P Bork; N P Brown; W S Hayes; Mark Borodovsky; Kenneth E Rudd; Eugene V Koonin
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.
Current biology : CB 1996;6(3):279-91.
1996: Eugene V Koonin; Kenneth E Rudd
Two domains of superfamily I helicases may exist as separate proteins.
Protein science : a publication of the Protein Society 1996;5(1):178-80.
1996: Eugene V Koonin; Roman L Tatusov; Kenneth E Rudd
Protein sequence comparison at genome scale.
Methods in enzymology 1996;266():295-322.
1995: Eugene V Koonin; Roman L Tatusov; Kenneth E Rudd
Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(25):11921-5.
1995: S Hannenhalli; Colombe Chappey; Eugene V Koonin; P A Pevzner
Genome sequence comparison and scenarios for gene rearrangements: a test case.
Genomics 1995;30(2):299-311.
1995: Eugene V Koonin; S Zhou; John C Lucchesi
The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin.
Nucleic acids research 1995;23(21):4229-33.
1995: Mark Borodovsky; J D McIninch; Eugene V Koonin; Kenneth E Rudd; C Médigue; Antoine Danchin
Detection of new genes in a bacterial genome using Markov models for three gene classes.
Nucleic acids research 1995;23(17):3554-62.
1995: Eugene V Koonin
Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF-2B subunits revealed by analysis of conserved sequence motifs.
Protein science : a publication of the Protein Society 1995;4(8):1608-17.
1995: Alexander V Karasev; V P Boyko; Siddarame Gowda; O V Nikolaeva; Mark E Hilf; Eugene V Koonin; C L Niblett; K Cline; D J Gumpf; R F Lee
Complete sequence of the citrus tristeza virus RNA genome.
Virology 1995;208(2):511-20.
1995: V A Klaassen; M L Boeshore; Eugene V Koonin; Tongyan Tian; Bryce W Falk
Genome structure and phylogenetic analysis of lettuce infectious yellows virus, a whitefly-transmitted, bipartite closterovirus.
Virology 1995;208(1):99-110.
1995: Eugene V Koonin
A protein splice-junction motif in hedgehog family proteins.
Trends in biochemical sciences 1995;20(4):141-2.
1995: Eugene V Koonin; S M van der Vies
Conserved sequence motifs in bacterial and bacteriophage chaperonins.
Trends in biochemical sciences 1995;20(1):14-5.
1995: Kenneth E Rudd; Heidi Sofia; Eugene V Koonin; Guy Plunkett; S Lazar; P E Rouviere
A new family of peptidyl-prolyl isomerases.
Trends in biochemical sciences 1995;20(1):12-4.
1994: Roman L Tatusov; Stephen F Altschul; Eugene V Koonin
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(25):12091-5.
1994: Eugene V Koonin; Roman L Tatusov
Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search.
Journal of molecular biology 1994;244(1):125-32.
1994: Mark Borodovsky; Kenneth E Rudd; Eugene V Koonin
Intrinsic and extrinsic approaches for detecting genes in a bacterial genome.
Nucleic acids research 1994;22(22):4756-67.
1994: Eugene V Koonin; AR Mushegian; Roman L Tatusov; Stephen F Altschul; S H Bryant; P Bork; A Valencia
Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain--study of a diverse, ancient protein superfamily using motif search and structural modeling.
Protein science : a publication of the Protein Society 1994;3(11):2045-54.
1994: A R Mushegian; H K Edskes; Eugene V Koonin
Eukaryotic RNAse H shares a conserved domain with caulimovirus proteins that facilitate translation of polycistronic RNA.
Nucleic acids research 1994;22(20):4163-6.
1994: Mark Borodovsky; Eugene V Koonin; Kenneth E Rudd
New genes in old sequence: a strategy for finding genes in the bacterial genome.
Trends in biochemical sciences 1994;19(8):309-13.
1994: Eugene V Koonin
Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120.
Nucleic acids research 1994;22(13):2476-8.
1994: A R Mushegian; Eugene V Koonin
Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity.
Protein science : a publication of the Protein Society 1994;3(7):1081-8.
1994: Roman L Tatusov; Eugene V Koonin
A simple tool to search for sequence motifs that are conserved in BLAST outputs.
Computer applications in the biosciences : CABIOS 1994;10(4):457-9.
1994: Eugene V Koonin; P Bork; Chris Sander
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
Nucleic acids research 1994;22(11):2166-7.
1994: Alexander V Karasev; O V Nikolaeva; Eugene V Koonin; D J Gumpf; SM Garnsey
Screening of the closterovirus genome by degenerate primer-mediated polymerase chain reaction.
The Journal of general virology 1994;75 ( Pt 6)():1415-22.
1994: Eugene V Koonin
Yeast protein controlling inter-organelle communication is related to bacterial phosphatases containing the Hsp 70-type ATP-binding domain.
Trends in biochemical sciences 1994;19(4):156-7.
1994: Eugene V Koonin; Kenneth E Rudd
A conserved domain in putative bacterial and bacteriophage transglycosylases.
Trends in biochemical sciences 1994;19(3):106-7.
1994: Eugene V Koonin; P Bork; Chris Sander
Yeast chromosome III: new gene functions.
The EMBO journal 1994;13(3):493-503.
1994: Eugene V Koonin
Conserved sequence pattern in a wide variety of phosphoesterases.
Protein science : a publication of the Protein Society 1994;3(2):356-8.
1994: Alexey A Agranovsky; Eugene V Koonin; V P Boyko; Edgar Maiss; R Frötschl; N A Lunina; Joseph G Atabekov
Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease.
Virology 1994;198(1):311-24.
1993: Eugene V Koonin; Kenneth E Rudd
SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases.
Nucleic acids research 1993;21(23):5519.
1993: Eugene V Koonin
A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses.
Nucleic acids research 1993;21(20):4847.
1993: T G Senkevich; G L Muravnik; S G Pozdnyakov; V E Chizhikov; O I Ryazankina; Sergei N Shchelkunov; Eugene V Koonin; V I Chernos
Nucleotide sequence of XhoI O fragment of ectromelia virus DNA reveals significant differences from vaccinia virus.
Virus research 1993;30(1):73-88.
1993: Eugene V Koonin; T G Senkevich
Fowlpox virus encodes a protein related to human deoxycytidine kinase: further evidence for independent acquisition of genes for enzymes of nucleotide metabolism by different viruses.
Virus genes 1993;7(3):289-95.
1993: Eugene V Koonin
A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication.
Nucleic acids research 1993;21(11):2541-7.
1993: Eugene V Koonin; Murray P Deutscher
RNase T shares conserved sequence motifs with DNA proofreading exonucleases.
Nucleic acids research 1993;21(10):2521-2.
1993: Eugene V Koonin
Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda 2 protein of reovirus.
The Journal of general virology 1993;74 ( Pt 4)():733-40.
1993: Eugene V Koonin
Escherichia coli dinG gene encodes a putative DNA helicase related to a group of eukaryotic helicases including Rad3 protein.
Nucleic acids research 1993;21(6):1497.
1993: Eugene V Koonin
A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif.
Journal of molecular biology 1993;229(4):1165-74.
1993: Eugene V Koonin; T G Senkevich; V I Chernos
Gene A32 product of vaccinia virus may be an ATPase involved in viral DNA packaging as indicated by sequence comparisons with other putative viral ATPases.
Virus genes 1993;7(1):89-94.
1993: Eugene V Koonin; Valerian V Dolja
Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences.
Critical reviews in biochemistry and molecular biology 1993;28(5):375-430.
1993: A R Mushegian; Eugene V Koonin
Cell-to-cell movement of plant viruses. Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems.
Archives of virology 1993;133(3-4):239-57.
1992: Eugene V Koonin
A new group of putative RNA helicases.
Trends in biochemical sciences 1992;17(12):495-7.
1992: Eugene V Koonin
The second cholera toxin, Zot, and its plasmid-encoded and phage-encoded homologues constitute a group of putative ATPases with an altered purine NTP-binding motif.
FEBS letters 1992;312(1):3-6.
1992: V P Boyko; Alexander V Karasev; Alexey A Agranovsky; Eugene V Koonin; Valerian V Dolja
Coat protein gene duplication in a filamentous RNA virus of plants.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(19):9156-60.
1992: T J Choi; S Kuwata; Eugene V Koonin; L A Heaton; Andrew O Jackson
Structure of the L (polymerase) protein gene of sonchus yellow net virus.
Virology 1992;189(1):31-9.
1992: Eugene V Koonin; T G Senkevich; V I Chernos
A family of DNA virus genes that consists of fused portions of unrelated cellular genes.
Trends in biochemical sciences 1992;17(6):213-4.
1992: Eugene V Koonin
DnaC protein contains a modified ATP-binding motif and belongs to a novel family of ATPases including also DnaA.
Nucleic acids research 1992;20(8):1997.
1992: T V Ilyina; A E Gorbalenya; Eugene V Koonin
Organization and evolution of bacterial and bacteriophage primase-helicase systems.
Journal of molecular evolution 1992;34(4):351-7.
1992: Eugene V Koonin; T G Senkevich
Vaccinia virus encodes four putative DNA and/or RNA helicases distantly related to each other.
The Journal of general virology 1992;73 ( Pt 4)():989-93.
1992: Eugene V Koonin; T G Senkevich
Evolution of thymidine and thymidylate kinases: the possibility of independent capture of TK genes by different groups of viruses.
Virus genes 1992;6(2):187-96.
1992: Eugene V Koonin
Archaebacterial virus SSV1 encodes a putative DnaA-like protein.
Nucleic acids research 1992;20(5):1143.
1992: Eugene V Koonin; A E Gorbalenya
An insect picornavirus may have genome organization similar to that of caliciviruses.
FEBS letters 1992;297(1-2):81-6.
1991: J Verchot; Eugene V Koonin; James C Carrington
The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase.
Virology 1991;185(2):527-35.
1991: Eugene V Koonin; G H Choi; Donald L Nuss; R Shapira; James C Carrington
Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(23):10647-51.
1991: Eugene V Koonin; AR Mushegian; Eugene Ryabov; Valerian V Dolja
Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity.
The Journal of general virology 1991;72 ( Pt 12)():2895-903.
1991: Valerian V Dolja; V P Boyko; Alexey A Agranovsky; Eugene V Koonin
Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation.
Virology 1991;184(1):79-86.
1991: Eugene V Koonin
Genome replication/expression strategies of positive-strand RNA viruses: a simple version of a combinatorial classification and prediction of new strategies.
Virus genes 1991;5(3):273-81.
1991: Eugene V Koonin; V P Boyko; Valerian V Dolja
Small cysteine-rich proteins of different groups of plant RNA viruses are related to different families of nucleic acid-binding proteins.
Virology 1991;181(1):395-8.
1991: Alexey A Agranovsky; V P Boyko; Alexander V Karasev; Eugene V Koonin; Valerian V Dolja
Putative 65 kDa protein of beet yellows closterovirus is a homologue of HSP70 heat shock proteins.
Journal of molecular biology 1991;217(4):603-10.
1991: Alexey A Agranovsky; V P Boyko; Alexander V Karasev; N A Lunina; Eugene V Koonin; Valerian V Dolja
Nucleotide sequence of the 3'-terminal half of beet yellows closterovirus RNA genome: unique arrangement of eight virus genes.
The Journal of general virology 1991;72 ( Pt 1)():15-23.
1989: Eugene V Koonin; A E Gorbalenya; K M Chumakov
Tentative identification of RNA-dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral polymerases.
FEBS letters 1989;252(1-2):42-6.