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Eugene Koonin

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.8 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Phenomena

Molecular Evolution

Concepts & Ideas

Genes & Molecular Sequences

Procedures

Sequence Alignment

Anatomy

Eukaryotic Cells

Living Beings

Chemicals & Drugs

Occupations

Computational Biology

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Co-Publications
Name
85
Wolf, Yuri
82
Aravind, L
68
Rogozin, Igor
60
Makarova, Kira
33
Galperin, Michael
22
Tatusov, Roman
16
Iyer, Lakshminarayan
16
Dolja, Valerian
15
Jordan, King
13
Kondrashov, Fyodor
11
Karev, Georgy
11
Carmel, Liran
11
Mushegian, AR
11
Omelchenko, Marina
11
Rudd, Kenneth

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Publications

TOP 3
Koonin Eugene V
The Origin at 150: is a new evolutionary synthesis in sight?
Irimia Manuel; Roy Scott William; Neafsey Daniel E; Abril Josep F; Garcia-Fernandez Jordi; Koonin Eugene V
Complex selection on 5' splice sites in intron-rich organisms.
Huang Yang; Koonin Eugene V; Lipman David J; Przytycka Teresa M
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.

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All Publications

2009: Koonin Eugene V
The Origin at 150: is a new evolutionary synthesis in sight?
Trends in genetics : TIG 2009;25(11):473-5.
2009: Irimia Manuel; Roy Scott William; Neafsey Daniel E; Abril Josep F; Garcia-Fernandez Jordi; Koonin Eugene V
Complex selection on 5' splice sites in intron-rich organisms.
Genome research 2009;19(11):2021-7.
2009: Huang Yang; Koonin Eugene V; Lipman David J; Przytycka Teresa M
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: Koonin Eugene V
On the origin of cells and viruses: primordial virus world scenario.
Annals of the New York Academy of Sciences 2009;1178():47-64.
2009: Senkevich Tatiana G; Koonin Eugene V; Moss Bernard
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: Sharon Itai; Alperovitch Ariella; Rohwer Forest; Haynes Matthew; Glaser Fabian; Atamna-Ismaeel Nof; Pinter Ron Y; Partensky Frédéric; Koonin Eugene V; Wolf Yuri I; Nelson Nathan; Béjà Oded
Photosystem I gene cassettes are present in marine virus genomes.
Nature 2009;461(7261):258-62.
2009: Koonin Eugene V
Intron-dominated genomes of early ancestors of eukaryotes.
The Journal of heredity 2009;100(5):618-23.
2009: Koonin Eugene V; Senkevich Tatiana G; Dolja Valerian V
Compelling reasons why viruses are relevant for the origin of cells.
Nature reviews. Microbiology 2009;7(8):615; author reply 615.
2009: Koonin Eugene V; Aravind L
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.
Cell cycle (Georgetown, Tex.) 2009;8(13):1984-5.
2009: Wolf Yuri I; Novichkov Pavel S; Karev Georgy P; Koonin Eugene V; Lipman David J
Inaugural Article: 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: Mulkidjanian Armen Y; Galperin Michael Y; Koonin Eugene V
Co-evolution of primordial membranes and membrane proteins.
Trends in biochemical sciences 2009;34(4):206-15.
2009: Koonin Eugene V
Towards a postmodern synthesis of evolutionary biology.
Cell cycle (Georgetown, Tex.) 2009;8(6):799-800.
2009: Koonin Eugene V
Darwinian evolution in the light of genomics.
Nucleic acids research 2009;37(4):1011-34.
2009: Koonin Eugene V; Novozhilov Artem S
Origin and evolution of the genetic code: the universal enigma.
IUBMB life 2009;61(2):99-111.
2009: Koonin Eugene V
Evolution of genome architecture.
The international journal of biochemistry & cell biology 2009;41(2):298-306.
2009: Novozhilov Artem S; Koonin Eugene V
Exceptional error minimization in putative primordial genetic codes.
Biology direct 2009;4():44.
2009: Koonin Eugene V; Wolf Yuri I
Is evolution Darwinian or/and Lamarckian?
Biology direct 2009;4():42.
2009: Blombach Fabian; Makarova Kira S; Marrero Jeannette; Siebers Bettina; Koonin Eugene V; van der Oost John
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: Koonin Eugene V; Wolf Yuri I
The fundamental units, processes and patterns of evolution, and the tree of life conundrum.
Biology direct 2009;4():33.
2009: Makarova Kira S; Wolf Yuri I; van der Oost John; Koonin Eugene V
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: Puigbò Pere; Wolf Yuri I; Koonin Eugene V
Search for a 'Tree of Life' in the thicket of the phylogenetic forest.
Journal of biology 2009;8(6):59.
2009: Makarova Kira S; Wolf Yuri I; Koonin Eugene V
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.
Biology direct 2009;4():19.
2009: Ng C Leong; Waterman David G; Koonin Eugene V; Walters Alison D; Chong James P J; Isupov Michail N; Lebedev Andrey A; Bunka David H J; Stockley Peter G; Ortiz-Lombardía Miguel; Antson Alfred A
Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein.
BMC structural biology 2009;9():32.
2009: Carmel Liran; Rogozin Igor B; Wolf Yuri I; Koonin Eugene V
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: Resch Alissa M; Ogurtsov Aleksey Y; Rogozin Igor B; Shabalina Svetlana A; Koonin Eugene V
Evolution of alternative and constitutive regions of mammalian 5'UTRs.
BMC genomics 2009;10():162.
2009: Tahirov Tahir H; Makarova Kira S; Rogozin Igor B; Pavlov Youri I; Koonin Eugene V
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: Yutin Natalya; Wolf Maxim Y; Wolf Yuri I; Koonin Eugene V
The origins of phagocytosis and eukaryogenesis.
Biology direct 2009;4():9.
2008: Koonin Eugene V; Wolf Yuri I; Nagasaki Keizo; Dolja Valerian V
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.
Nature reviews. Microbiology 2008;6(12):925-39.
2008: Koonin Eugene V; Wolf Yuri I
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.
Nucleic acids research 2008;36(21):6688-719.
2008: Basu Malay Kumar; Rogozin Igor B; Koonin Eugene V
Primordial spliceosomal introns were probably U2-type.
Trends in genetics : TIG 2008;24(11):525-8.
2008: Baranovskiy Andrey G; Babayeva Nigar D; Liston Victoria G; Rogozin Igor B; Koonin Eugene V; Pavlov Youri I; Vassylyev Dmitry G; Tahirov Tahir H
X-ray structure of the complex of regulatory subunits of human DNA polymerase delta.
Cell cycle (Georgetown, Tex.) 2008;7(19):3026-36.
2008: Assis Raquel; Kondrashov Alexey S; Koonin Eugene V; Kondrashov Fyodor A
Nested genes and increasing organizational complexity of metazoan genomes.
Trends in genetics : TIG 2008;24(10):475-8.
2008: van den Born Erwin; Omelchenko Marina V; Bekkelund Anders; Leihne Vibeke; Koonin Eugene V; Dolja Valerian V; Falnes Pål Ø
Viral AlkB proteins repair RNA damage by oxidative demethylation.
Nucleic acids research 2008;36(17):5451-61.
2008: Shabalina Svetlana A; Koonin Eugene V
Origins and evolution of eukaryotic RNA interference.
Trends in ecology & evolution (Personal edition) 2008;23(10):578-87.
2008: Brouns Stan J J; Jore Matthijs M; Lundgren Magnus; Westra Edze R; Slijkhuis Rik J H; Snijders Ambrosius P L; Dickman Mark J; Makarova Kira S; Koonin Eugene V; van der Oost John
Small CRISPR RNAs guide antiviral defense in prokaryotes.
Science (New York, N.Y.) 2008;321(5891):960-4.
2008: Yutin Natalya; Makarova Kira S; Mekhedov Sergey L; Wolf Yuri I; Koonin Eugene V
The deep archaeal roots of eukaryotes.
Molecular biology and evolution 2008;25(8):1619-30.
2008: Beloglazova Natalia; Brown Greg; Zimmerman Matthew D; Proudfoot Michael; Makarova Kira S; Kudritska Marina; Kochinyan Samvel; Wang Shuren; Chruszcz Maksymilian; Minor Wladek; Koonin Eugene V; Edwards Aled M; Savchenko Alexei; Yakunin Alexander F
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: Elkins James G; Podar Mircea; Graham David E; Makarova Kira S; Wolf Yuri; Randau Lennart; Hedlund Brian P; Brochier-Armanet Céline; Kunin Victor; Anderson Iain; Lapidus Alla; Goltsman Eugene; Barry Kerrie; Koonin Eugene V; Hugenholtz Phil; Kyrpides Nikos; Wanner Gerhard; Richardson Paul; Keller Martin; Stetter Karl O
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: Csurös Miklós; Rogozin Igor B; Koonin Eugene V
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: Senkevich Tatiana G; Wyatt Linda S; Weisberg Andrea S; Koonin Eugene V; Moss Bernard
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: Kosarek J Nicole; Woodruff Rachel V; Rivera-Begeman Amanda; Guo Caixia; D'Souza Sanjay; Koonin Eugene V; Walker Graham C; Friedberg Errol C
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: Basu Malay Kumar; Carmel Liran; Rogozin Igor B; Koonin Eugene V
Evolution of protein domain promiscuity in eukaryotes.
Genome research 2008;18(3):449-61.
2008: Avisar Dror; Prokhnevsky Alexey I; Makarova Kira S; Koonin Eugene V; Dolja Valerian V
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: Basu Malay Kumar; Rogozin Igor B; Deusch Oliver; Dagan Tal; Martin William; Koonin Eugene V
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.
2008: Saw Jimmy H; Mountain Bruce W; Feng Lu; Omelchenko Marina V; Hou Shaobin; Saito Jennifer A; Stott Matthew B; Li Dan; Zhao Guang; Wu Junli; Galperin Michael Y; Koonin Eugene V; Makarova Kira S; Wolf Yuri I; Rigden Daniel J; Dunfield Peter F; Wang Lei; Alam Maqsudul
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1.
Genome biology 2008;9(11):R161.
2008: Podar Mircea; Anderson Iain; Makarova Kira S; Elkins James G; Ivanova Natalia; Wall Mark A; Lykidis Athanasios; Mavromatis Kostantinos; Sun Hui; Hudson Matthew E; Chen Wenqiong; Deciu Cosmin; Hutchison Don; Eads Jonathan R; Anderson Abraham; Fernandes Fillipe; Szeto Ernest; Lapidus Alla; Kyrpides Nikos C; Saier Milton H; Richardson Paul M; Rachel Reinhard; Huber Harald; Eisen Jonathan A; Koonin Eugene V; Keller Martin; Stetter Karl O
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.
Genome biology 2008;9(11):R158.
2008: Wolf Maxim Y; Wolf Yuri I; Koonin Eugene V
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution.
Biology direct 2008;3():40.
2008: Rogozin Igor B; Makarova Kira S; Pavlov Youri I; Koonin Eugene V
A highly conserved family of inactivated archaeal B family DNA polymerases.
Biology direct 2008;3():32.
2008: Churbanov Alexander; Winters-Hilt Stephen; Koonin Eugene V; Rogozin Igor B
Accumulation of GC donor splice signals in mammals.
Biology direct 2008;3():30.
2008: Hou Shaobin; Makarova Kira S; Saw Jimmy H W; Senin Pavel; Ly Benjamin V; Zhou Zhemin; Ren Yan; Wang Jianmei; Galperin Michael Y; Omelchenko Marina V; Wolf Yuri I; Yutin Natalya; Koonin Eugene V; Stott Matthew B; Mountain Bruce W; Crowe Michelle A; Smirnova Angela V; Dunfield Peter F; Feng Lu; Wang Lei; Alam Maqsudul
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: Basu Malay Kumar; Makalowski Wojciech; Rogozin Igor B; Koonin Eugene V
U12 intron positions are more strongly conserved between animals and plants than U2 intron positions.
Biology direct 2008;3():19.
2008: Mulkidjanian Armen Y; Galperin Michael Y; Makarova Kira S; Wolf Yuri I; Koonin Eugene V
Evolutionary primacy of sodium bioenergetics.
Biology direct 2008;3():13.
2008: Rogozin Igor B; Thomson Karen; Csürös Miklós; Carmel Liran; Koonin Eugene V
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: Podar Mircea; Wall Mark A; Makarova Kira S; Koonin Eugene V
The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system.
Biology direct 2008;3():2.
2007: Rogozin Igor B; Wolf Yuri I; Carmel Liran; Koonin Eugene V
Analysis of rare amino acid replacements supports the Coelomata clade.
Molecular biology and evolution 2007;24(12):2594-7.
2007: De Silva Frank S; Lewis Whitney; Berglund Peter; Koonin Eugene V; Moss Bernard
Poxvirus DNA primase.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(47):18724-9.
2007: Mulkidjanian Armen Y; Makarova Kira S; Galperin Michael Y; Koonin Eugene V
Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.
Nature reviews. Microbiology 2007;5(11):892-9.
2007: Zheng Jie; Rogozin Igor B; Koonin Eugene V; Przytycka Teresa M
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: Vitushkina Maria V; Rogozin Igor B; Jelkmann Wilhelm; Koonin Eugene V; Agranovsky Alexey A
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: Resch Alissa M; Carmel Liran; Mariño-Ramírez Leonardo; Ogurtsov Aleksey Y; Shabalina Svetlana A; Rogozin Igor B; Koonin Eugene V
Widespread positive selection in synonymous sites of mammalian genes.
Molecular biology and evolution 2007;24(8):1821-31.
2007: Carmel Liran; Rogozin Igor B; Wolf Yuri I; Koonin Eugene V
Evolutionarily conserved genes preferentially accumulate introns.
Genome research 2007;17(7):1045-50.
2007: Carmel Liran; Wolf Yuri I; Rogozin Igor B; Koonin Eugene V
Three distinct modes of intron dynamics in the evolution of eukaryotes.
Genome research 2007;17(7):1034-44.
2007: Koonin Eugene V
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: Koonin Eugene V
Metagenomic sorcery and the expanding protein universe.
Nature biotechnology 2007;25(5):540-2.
2007: Martin William; Dagan Tal; Koonin Eugene V; Dipippo Jonathan L; Gogarten J Peter; Lake James A
The evolution of eukaryotes.
Science (New York, N.Y.) 2007;316(5824):542-3; author reply 542-3.
2007: Rogozin Igor B; Wolf Yuri I; Carmel Liran; Koonin Eugene V
Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements.
Molecular biology and evolution 2007;24(4):1080-90.
2007: Sverdlov Alexander V; Csuros Miklos; Rogozin Igor B; Koonin Eugene V
A glimpse of a putative pre-intron phase of eukaryotic evolution.
Trends in genetics : TIG 2007;23(3):105-8.
2007: Makarova Kira S; Koonin Eugene V
Evolutionary genomics of lactic acid bacteria.
Journal of bacteriology 2007;189(4):1199-208.
2007: Koonin Eugene V; Makarova Kira S; Elkins James G
Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".
Biology direct 2007;2():38.
2007: Makarova Kira S; Sorokin Alexander V; Novichkov Pavel S; Wolf Yuri I; Koonin Eugene V
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
Biology direct 2007;2():33.
2007: Novozhilov Artem S; Wolf Yuri I; Koonin Eugene V
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: Carmel Liran; Rogozin Igor B; Wolf Yuri I; Koonin Eugene V
Patterns of intron gain and conservation in eukaryotic genes.
BMC evolutionary biology 2007;7():192.
2007: Makarova Kira S; Omelchenko Marina V; Gaidamakova Elena K; Matrosova Vera Y; Vasilenko Alexander; Zhai Min; Lapidus Alla; Copeland Alex; Kim Edwin; Land Miriam; Mavrommatis Konstantinos; Pitluck Samuel; Richardson Paul M; Detter Chris; Brettin Thomas; Saunders Elizabeth; Lai Barry; Ravel Bruce; Kemner Kenneth M; Wolf Yuri I; Sorokin Alexander; Gerasimova Anna V; Gelfand Mikhail S; Fredrickson James K; Koonin Eugene V; Daly Michael J
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
PloS one 2007;2(9):e955.
2007: Koonin Eugene V
The Biological Big Bang model for the major transitions in evolution.
Biology direct 2007;2():21.
2007: Koonin Eugene V
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: Wolf Yuri I; Koonin Eugene V
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: Koonin Eugene V
Chance and necessity in cellular response to challenge.
Molecular systems biology 2007;3():107.
2006: Shakhnovich Boris E; Koonin Eugene V
Origins and impact of constraints in evolution of gene families.
Genome research 2006;16(12):1529-36.
2006: Correia Frederick F; D'Onofrio Anthony; Rejtar Tomas; Li Lingyun; Karger Barry L; Makarova Kira; Koonin Eugene V; Lewis Kim
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: Kuznetsova Ekaterina; Proudfoot Michael; Gonzalez Claudio F; Brown Greg; Omelchenko Marina V; Borozan Ivan; Carmel Liran; Wolf Yuri I; Mori Hirotada; Savchenko Alexei V; Arrowsmith Cheryl H; Koonin Eugene V; Edwards Aled M; Yakunin Alexander F
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: Makarova Kira S; Grishin Nick V; Koonin Eugene V
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinformatics (Oxford, England) 2006;22(21):2581-4.
2006: Koonin Eugene V; Wolf Yuri I
Evolutionary systems biology: links between gene evolution and function.
Current opinion in biotechnology 2006;17(5):481-7.
2006: Martin William; Koonin Eugene V
A positive definition of prokaryotes.
Nature 2006;442(7105):868.
2006: Mulkidjanian Armen Y; Koonin Eugene V; Makarova Kira S; Mekhedov Sergey L; Sorokin Alexander; Wolf Yuri I; Dufresne Alexis; Partensky Frédéric; Burd Henry; Kaznadzey Denis; Haselkorn Robert; Galperin Michael Y
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: Wolf Yuri I; Carmel Liran; Koonin Eugene V
Unifying measures of gene function and evolution.
Proceedings. Biological sciences / The Royal Society 2006;273(1593):1507-15.
2006: Aravind L; Iyer Lakshminarayan M; Koonin Eugene V
Comparative genomics and structural biology of the molecular innovations of eukaryotes.
Current opinion in structural biology 2006;16(3):409-19.
2006: Makarova Kira S; Koonin Eugene V; Haselkorn Robert; Galperin Michael Y
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: Marinsek Nina; Barry Elizabeth R; Makarova Kira S; Dionne Isabelle; Koonin Eugene V; Bell Stephen D
GINS, a central nexus in the archaeal DNA replication fork.
EMBO reports 2006;7(5):539-45.
2006: Prangishvili David; Garrett Roger A; Koonin Eugene V
Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life.
Virus research 2006;117(1):52-67.
2006: Koonin Eugene V; Dolja Valerian V
Evolution of complexity in the viral world: the dawn of a new vision.
Virus research 2006;117(1):1-4.
2006: Iyer Lakshminarayan M; Balaji S; Koonin Eugene V; Aravind L
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.
Virus research 2006;117(1):156-84.
2006: Novozhilov Artem S; Karev Georgy P; Koonin Eugene V
Biological applications of the theory of birth-and-death processes.
Briefings in bioinformatics 2006;7(1):70-85.
2006: Martin William; Koonin Eugene V
Introns and the origin of nucleus-cytosol compartmentalization.
Nature 2006;440(7080):41-5.
2006: Chiba Marin; Reed Jonathan C; Prokhnevsky Alexey I; Chapman Elisabeth J; Mawassi Munir; Koonin Eugene V; Carrington James C; Dolja Valerian V
Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon.
Virology 2006;346(1):7-14.
2006: Waterman David G; Ortiz-Lombardía Miguel; Fogg Mark J; Koonin Eugene V; Antson Alfred A
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: Koonin Eugene V
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases.
Biology direct 2006;1():39.
2006: Dewey Colin N; Rogozin Igor B; Koonin Eugene V
Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns.
BMC genomics 2006;7():311.
2006: Wolf Yuri I; Viboud Cecile; Holmes Edward C; Koonin Eugene V; Lipman David J
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus.
Biology direct 2006;1():34.
2006: Kondrashov Fyodor A; Koonin Eugene V; Morgunov Igor G; Finogenova Tatiana V; Kondrashova Marie N
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation.
Biology direct 2006;1():31.
2006: Karev Georgy P; Novozhilov Artem S; Koonin Eugene V
Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics.
Biology direct 2006;1():30.
2006: Koonin Eugene V; Senkevich Tatiana G; Dolja Valerian V
The ancient Virus World and evolution of cells.
Biology direct 2006;1():29.
2006: Tsaparas Panayiotis; Mariño-Ramírez Leonardo; Bodenreider Olivier; Koonin Eugene V; Jordan I King
Global similarity and local divergence in human and mouse gene co-expression networks.
BMC evolutionary biology 2006;6():70.
2006: Koonin Eugene V
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: Leebens-Mack Jim; Vision Todd; Brenner Eric; Bowers John E; Cannon Steven; Clement Mark J; Cunningham Clifford W; dePamphilis Claude; deSalle Rob; Doyle Jeff J; Eisen Jonathan A; Gu Xun; Harshman John; Jansen Robert K; Kellogg Elizabeth A; Koonin Eugene V; Mishler Brent D; Philippe Hervé; Pires J Chris; Qiu Yin-Long; Rhee Seung Y; Sjölander Kimmen; Soltis Douglas E; Soltis Pamela S; Stevenson Dennis W; Wall Kerr; Warnow Tandy; Zmasek Christian
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: Makarova Kira S; Grishin Nick V; Shabalina Svetlana A; Wolf Yuri I; Koonin Eugene V
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: Koonin Eugene V; Landweber Laura F; Lipman David J
A community experiment with fully open and published peer review.
Biology direct 2006;1():1.
2006: Novozhilov Artem S; Berezovskaya Faina S; Koonin Eugene V; Karev Georgy P
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: Glazko Galina V; Babenko Vladimir N; Koonin Eugene V; Rogozin Igor B
Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection.
Biology direct 2006;1():4.
2006: Babenko Vladimir N; Basu Malay K; Kondrashov Fyodor A; Rogozin Igor B; Koonin Eugene V
Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis.
BMC cancer 2006;6():36.
2005: Koonin Eugene V; Martin William
On the origin of genomes and cells within inorganic compartments.
Trends in genetics : TIG 2005;21(12):647-54.
2005: Karev Georgy P; Berezovskaya Faina S; Koonin Eugene V
Modeling genome evolution with a diffusion approximation of a birth-and-death process.
Bioinformatics (Oxford, England) 2005;21 Suppl 3():iii12-9.
2005: Makarova Kira S; Koonin Eugene V
Evolutionary and functional genomics of the Archaea.
Current opinion in microbiology 2005;8(5):586-94.
2005: Koonin Eugene V
Paralogs and mutational robustness linked through transcriptional reprogramming.
BioEssays : news and reviews in molecular, cellular and developmental biology 2005;27(9):865-8.
2005: Rogozin Igor B; Basu Malay K; Jordan I King; Pavlov Youri I; Koonin Eugene V
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: Kravchenko Julia E; Rogozin Igor B; Koonin Eugene V; Chumakov Peter M
Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin.
Nature 2005;436(7051):735-9.
2005: Novozhilov Artem S; Karev Georgy P; Koonin Eugene V
Mathematical modeling of evolution of horizontally transferred genes.
Molecular biology and evolution 2005;22(8):1721-32.
2005: Basu Malay K; Koonin Eugene V
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: Rogozin Igor B; Sverdlov Alexander V; Babenko Vladimir N; Koonin Eugene V
Analysis of evolution of exon-intron structure of eukaryotic genes.
Briefings in bioinformatics 2005;6(2):118-34.
2005: Koonin Eugene V; Rogozin Igor B; Glazko Galina V
p53 gain-of-function: tumor biology and bioinformatics come together.
Cell cycle (Georgetown, Tex.) 2005;4(5):686-8.
2005: Koonin Eugene V
Virology: Gulliver among the Lilliputians.
Current biology : CB 2005;15(5):R167-9.
2005: Moroz Olga V; Murzin Alexey G; Makarova Kira S; Koonin Eugene V; Wilson Keith S; Galperin Michael Y
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: Ulrich Luke E; Koonin Eugene V; Zhulin Igor B
One-component systems dominate signal transduction in prokaryotes.
Trends in microbiology 2005;13(2):52-6.
2005: Glazko Galina V; Koonin Eugene V; Rogozin Igor B
Molecular dating: ape bones agree with chicken entrails.
Trends in genetics : TIG 2005;21(2):89-92.
2005: Jordan I King; Kondrashov Fyodor A; Adzhubei Ivan A; Wolf Yuri I; Koonin Eugene V; Kondrashov Alexey S; Sunyaev Shamil
A universal trend of amino acid gain and loss in protein evolution.
Nature 2005;433(7026):633-8.
2005: Ng Chyan Leong; Waterman David; Koonin Eugene V; Antson Alfred A; Ortiz-Lombardía Miguel
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: Jordan I King; Mariño-Ramírez Leonardo; Koonin Eugene V
Evolutionary significance of gene expression divergence.
Gene 2005;345(1):119-26.
2005: Koonin Eugene V
Systemic determinants of gene evolution and function.
Molecular systems biology 2005;1():2005.0021.
2005: Koonin Eugene V
Orthologs, paralogs, and evolutionary genomics.
Annual review of genetics 2005;39():309-38.
2005: Omelchenko Marina V; Wolf Yuri I; Gaidamakova Elena K; Matrosova Vera Y; Vasilenko Alexander; Zhai Min; Daly Michael J; Koonin Eugene V; Makarova Kira S
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.
BMC evolutionary biology 2005;5():57.
2005: Churbanov Alexander; Rogozin Igor B; Babenko Vladimir N; Ali Hesham; Koonin Eugene V
Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes.
Nucleic acids research 2005;33(17):5512-20.
2005: Makarova Kira S; Wolf Yuri I; Mekhedov Sergey L; Mirkin Boris G; Koonin Eugene V
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.
Nucleic acids research 2005;33(14):4626-38.
2005: Iyer Lakshminarayan M; Koonin Eugene V; Leipe Detlef D; Aravind L
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: Sverdlov Alexander V; Rogozin Igor B; Babenko Vladimir N; Koonin Eugene V
Conservation versus parallel gains in intron evolution.
Nucleic acids research 2005;33(6):1741-8.
2004: Mans Ben J; Anantharaman Vivek; Aravind L; Koonin Eugene V
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.
Cell cycle (Georgetown, Tex.) 2004;3(12):1612-37.
2004: Hou Shaobin; Saw Jimmy H; Lee Kit Shan; Freitas Tracey A; Belisle Claude; Kawarabayasi Yutaka; Donachie Stuart P; Pikina Alla; Galperin Michael Y; Koonin Eugene V; Makarova Kira S; Omelchenko Marina V; Sorokin Alexander; Wolf Yuri I; Li Qing X; Keum Young Soo; Campbell Sonia; Denery Judith; Aizawa Shin-Ichi; Shibata Satoshi; Malahoff Alexander; Alam Maqsudul
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: Ettema Thijs J G; Makarova Kira S; Jellema Gera L; Gierman Hinco J; Koonin Eugene V; Huynen Martijn A; de Vos Willem M; van der Oost John
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: Iyer Lakshminarayan M; Koonin Eugene V; Aravind L
Novel predicted peptidases with a potential role in the ubiquitin signaling pathway.
Cell cycle (Georgetown, Tex.) 2004;3(11):1440-50.
2004: Jordan I King; Mariño-Ramírez Leonardo; Wolf Yuri I; Koonin Eugene V
Conservation and coevolution in the scale-free human gene coexpression network.
Molecular biology and evolution 2004;21(11):2058-70.
2004: Leipe Detlef D; Koonin Eugene V; Aravind L
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: Novichkov Pavel S; Omelchenko Marina V; Gelfand Mikhail S; Mironov Andrei A; Wolf Yuri I; Koonin Eugene V
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.
Journal of bacteriology 2004;186(19):6575-85.
2004: Karev Georgy P; Wolf Yuri I; Berezovskaya Faina S; Koonin Eugene V
Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models.
BMC evolutionary biology 2004;4():32.
2004: Sverdlov Alexander V; Rogozin Igor B; Babenko Vladimir N; Koonin Eugene V
Reconstruction of ancestral protosplice sites.
Current biology : CB 2004;14(16):1505-8.
2004: Sverdlov Alexander V; Babenko Vladimir N; Rogozin Igor B; Koonin Eugene V
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: Glazko Galina V; Koonin Eugene V; Rogozin Igor B
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: Wertz Ingrid E; O'Rourke Karen M; Zhou Honglin; Eby Michael; Aravind L; Seshagiri Somasekar; Wu Ping; Wiesmann Christian; Baker Rohan; Boone David L; Ma Averil; Koonin Eugene V; Dixit Vishva M
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling.
Nature 2004;430(7000):694-9.
2004: Jordan I King; Wolf Yuri I; Koonin Eugene V
Duplicated genes evolve slower than singletons despite the initial rate increase.
BMC evolutionary biology 2004;4():22.
2004: Iyer Lakshminarayan M; Aravind L; Coon Steven L; Klein David C; Koonin Eugene V
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: Kondrashov Fyodor A; Koonin Eugene V
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: Rogozin Igor B; Makarova Kira S; Wolf Yuri I; Koonin Eugene V
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes.
Briefings in bioinformatics 2004;5(2):131-49.
2004: Iyer Lakshminarayan M; Koonin Eugene V; Aravind L
Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer.
Gene 2004;335():73-88.
2004: Budanov Andrei V; Sablina Anna A; Feinstein Elena; Koonin Eugene V; Chumakov Peter M
Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD.
Science (New York, N.Y.) 2004;304(5670):596-600.
2004: Iyer Lakshminarayan M; Leipe Detlef D; Koonin Eugene V; Aravind L
Evolutionary history and higher order classification of AAA+ ATPases.
Journal of structural biology 2004;146(1-2):11-31.
2004: Sík Attila; Passer Brent J; Koonin Eugene V; Pellegrini Luca
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: Kouprina Natalay; Mullokandov Michael; Rogozin Igor B; Collins N Keith; Solomon Greg; Otstot John; Risinger John I; Koonin Eugene V; Barrett J Carl; Larionov Vladimir
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: Koonin Eugene V
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: Koonin Eugene V
Eugene V. Koonin.
Current biology : CB 2004;14(3):R96-7.
2004: Wolf Yuri I; Rogozin Igor B; Koonin Eugene V
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.
Genome research 2004;14(1):29-36.
2004: Galperin Michael Y; Koonin Eugene V
'Conserved hypothetical' proteins: prioritization of targets for experimental study.
Nucleic acids research 2004;32(18):5452-63.
2004: Iyer Lakshminarayan M; Makarova Kira S; Koonin Eugene V; Aravind L
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: Babenko Vladimir N; Rogozin Igor B; Mekhedov Sergei L; Koonin Eugene V
Prevalence of intron gain over intron loss in the evolution of paralogous gene families.
Nucleic acids research 2004;32(12):3724-33.
2004: Aravind L; Iyer Lakshminarayan M; Leipe Detlef D; Koonin Eugene V
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: Shabalina Svetlana A; Ogurtsov Aleksey Y; Rogozin Igor B; Koonin Eugene V; Lipman David J
Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.
Nucleic acids research 2004;32(5):1774-82.
2004: Koonin Eugene V; Fedorova Natalie D; Jackson John D; Jacobs Aviva R; Krylov Dmitri M; Makarova Kira S; Mazumder Raja; Mekhedov Sergei L; Nikolskaya Anastasia N; Rao B Sridhar; Rogozin Igor B; Smirnov Sergei; Sorokin Alexander V; Sverdlov Alexander V; Vasudevan Sona; Wolf Yuri I; Yin Jodie J; Natale Darren A
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Genome biology 2004;5(2):R7.
2003: Sverdlov Alexander V; Rogozin Igor B; Babenko Vladimir N; Koonin Eugene V
Evidence of splice signal migration from exon to intron during intron evolution.
Current biology : CB 2003;13(24):2170-4.
2003: Koonin Eugene V
Comparative genomics, minimal gene-sets and the last universal common ancestor.
Nature reviews. Microbiology 2003;1(2):127-36.
2003: Koonin Eugene V
Horizontal gene transfer: the path to maturity.
Molecular microbiology 2003;50(3):725-7.
2003: Leipe Detlef D; Koonin Eugene V; Aravind L
Evolution and classification of P-loop kinases and related proteins.
Journal of molecular biology 2003;333(4):781-815.
2003: Makarova Kira S; Koonin Eugene V
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: Karev Georgy P; Wolf Yuri I; Koonin Eugene V
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: Krylov Dmitri M; Wolf Yuri I; Rogozin Igor B; Koonin Eugene V
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.
Genome research 2003;13(10):2229-35.
2003: Tatusov Roman L; Fedorova Natalie D; Jackson John D; Jacobs Aviva R; Kiryutin Boris; Koonin Eugene V; Krylov Dmitri M; Mazumder Raja; Mekhedov Sergei L; Nikolskaya Anastasia N; Rao B Sridhar; Smirnov Sergei; Sverdlov Alexander V; Vasudevan Sona; Wolf Yuri I; Yin Jodie J; Natale Darren A
The COG database: an updated version includes eukaryotes.
BMC bioinformatics 2003;4():41.
2003: Rogozin Igor B; Wolf Yuri I; Sorokin Alexander V; Mirkin Boris G; Koonin Eugene V
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: Dufresne Alexis; Salanoubat Marcel; Partensky Frédéric; Artiguenave François; Axmann Ilka M; Barbe Valérie; Duprat Simone; Galperin Michael Y; Koonin Eugene V; Le Gall Florence; Makarova Kira S; Ostrowski Martin; Oztas Sophie; Robert Catherine; Rogozin Igor B; Scanlan David J; Tandeau de Marsac Nicole; Weissenbach Jean; Wincker Patrick; Wolf Yuri I; Hess Wolfgang R
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: Makarova Kira S; Wolf Yuri I; Koonin Eugene V
Potential genomic determinants of hyperthermophily.
Trends in genetics : TIG 2003;19(4):172-6.
2003: Liu Yongqing; Zhou Jizhong; Omelchenko Marina V; Beliaev Alex S; Venkateswaran Amudhan; Stair Julia; Wu Liyou; Thompson Dorothea K; Xu Dong; Rogozin Igor B; Gaidamakova Elena K; Zhai Min; Makarova Kira S; Koonin Eugene V; Daly Michael J
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: Aravind L; Iyer L M; Koonin E V
Scores of RINGS but no PHDs in ubiquitin signaling.
Cell cycle (Georgetown, Tex.) 2003;2(2):123-6.
2003: Yang Wei; Rogozin Igor B; Koonin Eugene V
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: Koonin Eugene V
Swift publication would reward good reviewers.
Nature 2003;422(6930):374.
2003: Glazko Galina V; Koonin Eugene V; Rogozin Igor B; Shabalina Svetlana A
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: Kondrashov Fyodor A; Koonin Eugene V
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: Rogozin Igor B; Aravind L; Koonin Eugene V
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: Napuli Alberto J; Alzhanova Dina V; Doneanu Catalin E; Barofsky Douglas F; Koonin Eugene V; Dolja Valerian V
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: Jordan I King; Rogozin Igor B; Glazko Galina V; Koonin Eugene V
Origin of a substantial fraction of human regulatory sequences from transposable elements.
Trends in genetics : TIG 2003;19(2):68-72.
2003: Anantharaman Vivek; Aravind L; Koonin Eugene V
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins.
Current opinion in chemical biology 2003;7(1):12-20.
2003: Iyer Lakshminarayan M; Koonin Eugene V; Aravind L
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: Krylov Dmitri M; Nasmyth Kim; Koonin Eugene V
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: Jordan I King; Wolf Yuri I; Koonin Eugene V
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: Mirkin Boris G; Fenner Trevor I; Galperin Michael Y; Koonin Eugene V
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: Rogozin I B; Babenko V N; Fedorova N D; Jackson J D; Jacobs A R; Krylov D M; Makarova K S; Mazumder R; Mekhedov S L; Mirkin B G; Nikolskaya A N; Rao B S; Smirnov S; Sorokin A V; Sverdlov A V; Vasudevan S; Wolf Y I; Yin J J; Natale D A; Koonin E V
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: Omelchenko Marina V; Makarova Kira S; Wolf Yuri I; Rogozin Igor B; Koonin Eugene V
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.
Genome biology 2003;4(9):R55.
2003: Koonin Eugene V; Rogozin Igor B
Getting positive about selection.
Genome biology 2003;4(8):331.
2003: Makarova Kira S; Koonin Eugene V
Comparative genomics of Archaea: how much have we learned in six years, and what's next?
Genome biology 2003;4(8):115.
2003: Ponomarev Vladimir A; Makarova Kira S; Aravind L; Koonin Eugene V
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: Jordan I King; Henze Katrin; Fedorova Natalie D; Koonin Eugene V; Galperin Michael Y
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: Koonin Eugene V; Makarova Kira S; Rogozin Igor B; Davidovic Laetitia; Letellier Marie-Claude; Pellegrini Luca
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: Sonnhammer Erik L L; Koonin Eugene V
Orthology, paralogy and proposed classification for paralog subtypes.
Trends in genetics : TIG 2002;18(12):619-20.
2002: Koonin Eugene V; Wolf Yuri I; Karev Georgy P
The structure of the protein universe and genome evolution.
Nature 2002;420(6912):218-23.
2002: Lipman David J; Souvorov Alexander; Koonin Eugene V; Panchenko Anna R; Tatusova Tatiana A
The relationship of protein conservation and sequence length.
BMC evolutionary biology 2002;2():20.
2002: Rogozin Igor B; Makarova Kira S; Natale Darren A; Spiridonov Alexey N; Tatusov Roman L; Wolf Yuri I; Yin Jodie; Koonin Eugene V
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.
Nucleic acids research 2002;30(19):4264-71.
2002: Cope Gregory A; Suh Greg S B; Aravind L; Schwarz Sylvia E; Zipursky S Lawrence; Koonin Eugene V; Deshaies Raymond J
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: Verma Rati; Aravind L; Oania Robert; McDonald W Hayes; Yates John R; Koonin Eugene V; Deshaies Raymond J
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome.
Science (New York, N.Y.) 2002;298(5593):611-5.
2002: Senkevich Tatiana G; White Christine L; Weisberg Andrea; Granek Joshua A; Wolffe Elizabeth J; Koonin Eugene V; Moss Bernard
Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis.
Virology 2002;300(2):296-303.
2002: Daigle Denis M; Rossi Laura; Berghuis Albert M; Aravind L; Koonin Eugene V; Brown Eric D
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: Wolf Yuri I; Rogozin Igor B; Grishin Nick V; Koonin Eugene V
Genome trees and the tree of life.
Trends in genetics : TIG 2002;18(9):472-9.
2002: Makarova Kira S; Aravind L; Koonin Eugene V
SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes.
Trends in biochemical sciences 2002;27(8):384-6.
2002: Castillo-Davis Cristian I; Mekhedov Sergei L; Hartl Daniel L; Koonin Eugene V; Kondrashov Fyodor A
Selection for short introns in highly expressed genes.
Nature genetics 2002;31(4):415-8.
2002: Lespinet Olivier; Wolf Yuri I; Koonin Eugene V; Aravind L
The role of lineage-specific gene family expansion in the evolution of eukaryotes.
Genome research 2002;12(7):1048-59.
2002: Aravind L; Anantharaman Vivek; Koonin Eugene V
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: Jordan I King; Rogozin Igor B; Wolf Yuri I; Koonin Eugene V
Microevolutionary genomics of bacteria.
Theoretical population biology 2002;61(4):435-47.
2002: Aravind L; Mazumder Raja; Vasudevan Sona; Koonin Eugene V
Trends in protein evolution inferred from sequence and structure analysis.
Current opinion in structural biology 2002;12(3):392-9.
2002: Jordan I King; Rogozin Igor B; Wolf Yuri I; Koonin Eugene V
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria.
Genome research 2002;12(6):962-8.
2002: Rogozin Igor B; Spiridonov Alexey N; Sorokin Alexander V; Wolf Yuri I; Jordan I King; Tatusov Roman L; Koonin Eugene V
Purifying and directional selection in overlapping prokaryotic genes.
Trends in genetics : TIG 2002;18(5):228-32.
2002: Rogozin Igor B; Makarova Kira S; Murvai Janos; Czabarka Eva; Wolf Yuri I; Tatusov Roman L; Szekely Laszlo A; Koonin Eugene V
Connected gene neighborhoods in prokaryotic genomes.
Nucleic acids research 2002;30(10):2212-23.
2002: Senkevich Tatiana G; White Christine L; Koonin Eugene V; Moss Bernard
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: Omelchenko Marina V; Makarova Kira S; Koonin Eugene V
Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain.
FEMS microbiology letters 2002;209(2):255-60.
2002: Koonin E V; Aravind L
Origin and evolution of eukaryotic apoptosis: the bacterial connection.
Cell death and differentiation 2002;9(4):394-404.
2002: Slesarev Alexei I; Mezhevaya Katja V; Makarova Kira S; Polushin Nikolai N; Shcherbinina Olga V; Shakhova Vera V; Belova Galina I; Aravind L; Natale Darren A; Rogozin Igor B; Tatusov Roman L; Wolf Yuri I; Stetter Karl O; Malykh Andrei G; Koonin Eugene V; Kozyavkin Sergei A
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: Anantharaman Vivek; Koonin Eugene V; Aravind L
Comparative genomics and evolution of proteins involved in RNA metabolism.
Nucleic acids research 2002;30(7):1427-64.
2002: Leipe Detlef D; Wolf Yuri I; Koonin Eugene V; Aravind L
Classification and evolution of P-loop GTPases and related ATPases.
Journal of molecular biology 2002;317(1):41-72.
2002: Iyer Lakshminarayan M; Koonin Eugene V; Aravind L
Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52.
BMC genomics 2002;3(1):8.
2002: Aravind L; Koonin Eugene V
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: Wolf Yuri I; Karev Georgy; Koonin Eugene V
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: Makarova Kira S; Aravind L; Grishin Nick V; Rogozin Igor B; Koonin Eugene V
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
Nucleic acids research 2002;30(2):482-96.
2002: Béjà Oded; Koonin Eugene V; Aravind L; Taylor Lance T; Seitz Heidi; Stein Jefferey L; Bensen Daniel C; Feldman Robert A; Swanson Ronald V; DeLong Edward F
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: Anantharaman Vivek; Koonin Eugene V; Aravind L
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.
2002: Karev Georgy P; Wolf Yuri I; Rzhetsky Andrey Y; Berezovskaya Faina S; Koonin Eugene V
Birth and death of protein domains: a simple model of evolution explains power law behavior.
BMC evolutionary biology 2002;2(1):18.
2002: Yanai Itai; Wolf Yuri I; Koonin Eugene V
Evolution of gene fusions: horizontal transfer versus independent events.
Genome biology 2002;3(5):research0024.
2002: Iyer Lakshminarayan M; Koonin Eugene V; Aravind L
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: Kondrashov Fyodor A; Rogozin Igor B; Wolf Yuri I; Koonin Eugene V
Selection in the evolution of gene duplications.
Genome biology 2002;3(2):RESEARCH0008.
2001: Iyer L M; Aravind L; Koonin E V
Common origin of four diverse families of large eukaryotic DNA viruses.
Journal of virology 2001;75(23):11720-34.
2001: Kondrashov F A; Koonin E V
Origin of alternative splicing by tandem exon duplication.
Human molecular genetics 2001;10(23):2661-9.
2001: Avedisov S N; Rogozin I B; Koonin E V; Thomas B J
Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila.
Molecular biology and evolution 2001;18(11):2110-8.
2001: Wolf Y I; Rogozin I B; Grishin N V; Tatusov R L; Koonin E V
Genome trees constructed using five different approaches suggest new major bacterial clades.
BMC evolutionary biology 2001;1():8.
2001: Rogozin I B; Kochetov A V; Kondrashov F A; Koonin E V; Milanesi L
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: Wolf Y I; Kondrashov F A; Koonin E V
Footprints of primordial introns on the eukaryotic genome: still no clear traces.
Trends in genetics : TIG 2001;17(9):499-501.
2001: Galperin M Y; Nikolskaya A N; Koonin E V
Novel domains of the prokaryotic two-component signal transduction systems.
FEMS microbiology letters 2001;203(1):11-21.
2001: Krylov D M; Koonin E V
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: Anantharaman V; Koonin E V; Aravind L
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: Wolf Y I; Koonin E V
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: Aravind L; Koonin E V
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: Nölling J; Breton G; Omelchenko M V; Makarova K S; Zeng Q; Gibson R; Lee H M; Dubois J; Qiu D; Hitti J; Wolf Y I; Tatusov R L; Sabathe F; Doucette-Stamm L; Soucaille P; Daly M J; Bennett G N; Koonin E V; Smith D R
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.
Journal of bacteriology 2001;183(16):4823-38.
2001: Erokhina T N; Vitushkina M V; Zinovkin R A; Lesemann D E; Jelkmann W; Koonin E V; Agranovsky A A
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: Schäffer A A; Aravind L; Madden T L; Shavirin S; Spouge J L; Wolf Y I; Koonin E V; Altschul S F
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: Sreekumar K R; Aravind L; Koonin E V
Computational analysis of human disease-associated genes and their protein products.
Current opinion in genetics & development 2001;11(3):247-57.
2001: Iyer L M; Koonin E V; Aravind L
Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily.
Proteins 2001;43(2):134-44.
2001: Anantharaman V; Koonin E V; Aravind L
TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes.
FEMS microbiology letters 2001;197(2):215-21.
2001: Aravind L; Koonin E V
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: Anantharaman V; Koonin E V; Aravind L
Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.
Journal of molecular biology 2001;307(5):1271-92.
2001: Jordan I K; Makarova K S; Spouge J L; Wolf Y I; Koonin E V
Lineage-specific gene expansions in bacterial and archaeal genomes.
Genome research 2001;11(4):555-65.
2001: Koonin E V
Computational genomics.
Current biology : CB 2001;11(5):R155-8.
2001: Makarova K S; Aravind L; Wolf Y I; Tatusov R L; Minton K W; Koonin E V; Daly M J
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: Wolf Y I; Rogozin I B; Kondrashov A S; Koonin E V
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
Genome research 2001;11(3):356-72.
2001: Aravind L; Dixit V M; Koonin E V
Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons.
Science (New York, N.Y.) 2001;291(5507):1279-84.
2001: Koonin E V; Wolf Y I; Aravind L
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: Jordan I K; Makarova K S; Wolf Y I; Koonin E V
Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae.
Trends in genetics : TIG 2001;17(1):7-10.
2001: Tatusov R L; Natale D A; Garkavtsev I V; Tatusova T A; Shankavaram U T; Rao B S; Kiryutin B; Galperin M Y; Fedorova N D; Koonin E V
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Nucleic acids research 2001;29(1):22-8.
2001: Jordan I K; Kondrashov F A; Rogozin I B; Tatusov R L; Wolf Y I; Koonin E V
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
Genome biology 2001;2(12):RESEARCH0053.
2001: Iyer L M; Aravind L; Bork P; Hofmann K; Mushegian A R; Zhulin I B; Koonin E V
Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Genome biology 2001;2(12):RESEARCH0051.
2001: Makarova K S; Ponomarev V A; Koonin E V
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: Koonin E V; Makarova K S; Aravind L
Horizontal gene transfer in prokaryotes: quantification and classification.
Annual review of microbiology 2001;55():709-42.
2001: Galperin M Y; Koonin E V
Comparative genome analysis.
Methods of biochemical analysis 2001;43():359-92.
2001: Koonin E V
An apology for orthologs - or brave new memes.
Genome biology 2001;2(4):COMMENT1005.
2001: Aravind L; Koonin E V
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.
2000: Koonin E V; Aravind L
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: Béjà O; Suzuki M T; Koonin E V; Aravind L; Hadd A; Nguyen L P; Villacorta R; Amjadi M; Garrigues C; Jovanovich S B; Feldman R A; DeLong E F
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.
Environmental microbiology 2000;2(5):516-29.
2000: Koonin E V; Wolf Y I; Kondrashov A S; Aravind L
Bacterial homologs of the small subunit of eukaryotic DNA primase.
Journal of molecular microbiology and biotechnology 2000;2(4):509-12.
2000: Rogozin I B; Lyons-Weiler J; Koonin E V
Intron sliding in conserved gene families.
Trends in genetics : TIG 2000;16(10):430-2.
2000: Senkevich T G; White C L; Koonin E V; Moss B
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: Aravind L; Watanabe H; Lipman D J; Koonin E V
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: Béjà O; Aravind L; Koonin E V; Suzuki M T; Hadd A; Nguyen L P; Jovanovich S B; Gates C M; Feldman R A; Spudich J L; Spudich E N; DeLong E F
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.
Science (New York, N.Y.) 2000;289(5486):1902-6.
2000: Aravind L; Makarova K S; Koonin E V
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: Aravind L; Koonin E V
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: Wolf Y I; Kondrashov F A; Koonin E V
No footprints of primordial introns in a eukaryotic genome.
Trends in genetics : TIG 2000;16(8):333-4.
2000: Garcia A D; Aravind L; Koonin E V; Moss B
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: Grishin N V; Wolf Y I; Koonin E V
From complete genomes to measures of substitution rate variability within and between proteins.
Genome research 2000;10(7):991-1000.
2000: Wolf Y I; Grishin N V; Koonin E V
Estimating the number of protein folds and families from complete genome data.
Journal of molecular biology 2000;299(4):897-905.
2000: Galperin M Y; Koonin E V
Who's your neighbor? New computational approaches for functional genomics.
Nature biotechnology 2000;18(6):609-13.
2000: Aravind L; Koonin E V
SAP - a putative DNA-binding motif involved in chromosomal organization.
Trends in biochemical sciences 2000;25(3):112-4.
2000: Berman P; Zhang Z; Wolf Y I; Koonin E V; Miller W
Winnowing sequences from a database search.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):293-302.
2000: Galperin M Y; Aravind L; Koonin E V
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: Makarova K S; Aravind L; Koonin E V
A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae.
Trends in biochemical sciences 2000;25(2):50-2.
2000: Koonin E V
Bridging the gap between sequence and function.
Trends in genetics : TIG 2000;16(1):16.
2000: Leipe D D; Aravind L; Grishin N V; Koonin E V
The bacterial replicative helicase DnaB evolved from a RecA duplication.
Genome research 2000;10(1):5-16.
2000: Tatusov R L; Galperin M Y; Natale D A; Koonin E V
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Nucleic acids research 2000;28(1):33-6.
2000: Koonin E V
How many genes can make a cell: the minimal-gene-set concept.
Annual review of genomics and human genetics 2000;1():99-116.
2000: Wolf Y I; Kondrashov A S; Koonin E V
Interkingdom gene fusions.
Genome biology 2000;1(6):RESEARCH0013.
2000: Natale D A; Shankavaram U T; Galperin M Y; Wolf Y I; Aravind L; Koonin E V
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: Aravind L; Koonin E V
The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates.
Genome biology 2000;1(4):RESEARCH0007.
2000: Natale D A; Galperin M Y; Tatusov R L; Koonin E V
Using the COG database to improve gene recognition in complete genomes.
Genetica 2000;108(1):9-17.
2000: Makarova K S; Aravind L; Daly M J; Koonin E V
Specific expansion of protein families in the radioresistant bacterium Deinococcus radiodurans.
Genetica 2000;108(1):25-34.
2000: Koonin E V; Wolf Y I; Aravind L
Protein fold recognition using sequence profiles and its application in structural genomics.
Advances in protein chemistry 2000;54():245-75.
1999: Schäffer A A; Wolf Y I; Ponting C P; Koonin E V; Aravind L; Altschul S F
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: Galperin M Y; Koonin E V
Searching for drug targets in microbial genomes.
Current opinion in biotechnology 1999;10(6):571-8.
1999: Aravind L; Koonin E V
DNA-binding proteins and evolution of transcription regulation in the archaea.
Nucleic acids research 1999;27(23):4658-70.
1999: Galperin M Y; Natale D A; Aravind L; Koonin E V
A specialized version of the HD hydrolase domain implicated in signal transduction.
Journal of molecular microbiology and biotechnology 1999;1(2):303-5.
1999: Koonin E V; Aravind L; Hofmann K; Tschopp J; Dixit V M
Apoptosis. Searching for FLASH domains.
Nature 1999;401(6754):662; discussion 662-3.
1999: Aravind L; Koonin E V
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: Leipe D D; Aravind L; Koonin E V
Did DNA replication evolve twice independently?
Nucleic acids research 1999;27(17):3389-401.
1999: Makarova K S; Aravind L; Koonin E V
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: Wolf Y I; Aravind L; Grishin N V; Koonin E V
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: Makarova K S; Aravind L; Galperin M Y; Grishin N V; Tatusov R L; Wolf Y I; Koonin E V
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: Ponting C P; Aravind L; Schultz J; Bork P; Koonin E V
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Journal of molecular biology 1999;289(4):729-45.
1999: Wolf Y I; Aravind L; Koonin E V
Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange.
Trends in genetics : TIG 1999;15(5):173-5.
1999: Aravind L; Koonin E V
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches.
Journal of molecular biology 1999;287(5):1023-40.
1999: Aravind L; Koonin E V
DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.
Nucleic acids research 1999;27(7):1609-18.
1999: Aravind L; Koonin E V
Novel predicted RNA-binding domains associated with the translation machinery.
Journal of molecular evolution 1999;48(3):291-302.
1999: Aravind L; Walker D R; Koonin E V
Conserved domains in DNA repair proteins and evolution of repair systems.
Nucleic acids research 1999;27(5):1223-42.
1999: Aravind L; Dixit V M; Koonin E V
The domains of death: evolution of the apoptosis machinery.
Trends in biochemical sciences 1999;24(2):47-53.
1999: Wolf Y I; Brenner S E; Bash P A; Koonin E V
Distribution of protein folds in the three superkingdoms of life.
Genome research 1999;9(1):17-26.
1999: Aravind L; Koonin E V
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: Galperin M Y; Koonin E V
Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes.
Genetica 1999;106(1-2):159-70.
1998: Aravind L; Koonin E V
The HD domain defines a new superfamily of metal-dependent phosphohydrolases.
Trends in biochemical sciences 1998;23(12):469-72.
1998: Altschul S F; Koonin E V
Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.
Trends in biochemical sciences 1998;23(11):444-7.
1998: Leonard C J; Aravind L; Koonin E V
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: Aravind L; Leipe D D; Koonin E V
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: Zhang Z; Schäffer A A; Miller W; Madden T L; Lipman D J; Koonin E V; Altschul S F
Protein sequence similarity searches using patterns as seeds.
Nucleic acids research 1998;26(17):3986-90.
1998: Galperin M Y; Bairoch A; Koonin E V
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: Aravind L; Koonin E V
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: Galperin M Y; Walker D R; Koonin E V
Analogous enzymes: independent inventions in enzyme evolution.
Genome research 1998;8(8):779-90.
1998: Aravind L; Koonin E V
Phosphoesterase domains associated with DNA polymerases of diverse origins.
Nucleic acids research 1998;26(16):3746-52.
1998: Koonin E V; Tatusov R L; Galperin M Y
Beyond complete genomes: from sequence to structure and function.
Current opinion in structural biology 1998;8(3):355-63.
1998: Aravind L; Galperin M Y; Koonin E V
The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold.
Trends in biochemical sciences 1998;23(4):127-9.
1998: Koonin E V; Aravind L
Genomics: re-evaluation of translation machinery evolution.
Current biology : CB 1998;8(8):R266-9.
1998: Aravind L; Koonin E V
A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease.
Trends in biochemical sciences 1998;23(1):17-9.
1998: Galperin M Y; Koonin E V
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: Koonin E V; Mushegian A R; Dolja V V
Computer analysis of amino acid sequences. The case of plant virus capsid proteins.
Methods in molecular biology (Clifton, N.J.) 1998;81():319-37.
1997: Koonin E V; Galperin M Y
Prokaryotic genomes: the emerging paradigm of genome-based microbiology.
Current opinion in genetics & development 1997;7(6):757-63.
1997: Galperin M Y; Koonin E V
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: Tatusov R L; Koonin E V; Lipman D J
A genomic perspective on protein families.
Science (New York, N.Y.) 1997;278(5338):631-7.
1997: Koonin E V
Genome sequences: genome sequence of a model prokaryote.
Current biology : CB 1997;7(10):R656-9.
1997: Koonin E V; Mushegian A R; Galperin M Y; Walker D R
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: Senkevich T G; Koonin E V; Bugert J J; Darai G; Moss B
The genome of molluscum contagiosum virus: analysis and comparison with other poxviruses.
Virology 1997;233(1):19-42.
1997: Mushegian A R; Bassett D E; Boguski M S; Bork P; Koonin E V
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: Koonin E V
Big time for small genomes.
Genome research 1997;7(5):418-21.
1996: Koonin E V; Mushegian A R
Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics.
Current opinion in genetics & development 1996;6(6):757-62.
1996: Mushegian A R; Koonin E V
Sequence analysis of eukaryotic developmental proteins: ancient and novel domains.
Genetics 1996;144(2):817-28.
1996: Mushegian A R; Koonin E V
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: Koonin E V
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: Koonin E V
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: Koonin E V; Mushegian A R; Rudd K E
Sequencing and analysis of bacterial genomes.
Current biology : CB 1996;6(4):404-16.
1996: Koonin E V; Bork P
Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes.
Trends in biochemical sciences 1996;21(4):128-9.
1996: Tatusov R L; Mushegian A R; Bork P; Brown N P; Hayes W S; Borodovsky M; Rudd K E; Koonin E V
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.
Current biology : CB 1996;6(3):279-91.
1996: Koonin E V; Rudd K E
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: Koonin E V; Tatusov R L; Rudd K E
Protein sequence comparison at genome scale.
Methods in enzymology 1996;266():295-322.
1995: Koonin E V; Tatusov R L; Rudd K E
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: Hannenhalli S; Chappey C; Koonin E V; Pevzner P A
Genome sequence comparison and scenarios for gene rearrangements: a test case.
Genomics 1995;30(2):299-311.
1995: Koonin E V; Zhou S; Lucchesi J C
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: Borodovsky M; McIninch J D; Koonin E V; Rudd K E; Médigue C; Danchin A
Detection of new genes in a bacterial genome using Markov models for three gene classes.
Nucleic acids research 1995;23(17):3554-62.
1995: Koonin E V
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: Klaassen V A; Boeshore M L; Koonin E V; Tian T; Falk B W
Genome structure and phylogenetic analysis of lettuce infectious yellows virus, a whitefly-transmitted, bipartite closterovirus.
Virology 1995;208(1):99-110.
1995: Koonin E V
A protein splice-junction motif in hedgehog family proteins.
Trends in biochemical sciences 1995;20(4):141-2.
1995: Karasev A V; Boyko V P; Gowda S; Nikolaeva O V; Hilf M E; Koonin E V; Niblett C L; Cline K; Gumpf D J; Lee R F
Complete sequence of the citrus tristeza virus RNA genome.
Virology 1995;208(2):511-20.
1995: Koonin E V; van der Vies S M
Conserved sequence motifs in bacterial and bacteriophage chaperonins.
Trends in biochemical sciences 1995;20(1):14-5.
1995: Rudd K E; Sofia H J; Koonin E V; Plunkett G; Lazar S; Rouviere P E
A new family of peptidyl-prolyl isomerases.
Trends in biochemical sciences 1995;20(1):12-4.
1994: Tatusov R L; Altschul S F; Koonin E V
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: Borodovsky M; Rudd K E; Koonin E V
Intrinsic and extrinsic approaches for detecting genes in a bacterial genome.
Nucleic acids research 1994;22(22):4756-67.
1994: Koonin E V; Tatusov R L
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: Koonin E V; Mushegian A R; Tatusov R L; Altschul S F; Bryant S H; Bork P; Valencia A
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: Mushegian A R; Edskes H K; Koonin E V
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: Borodovsky M; Koonin E V; Rudd K E
New genes in old sequence: a strategy for finding genes in the bacterial genome.
Trends in biochemical sciences 1994;19(8):309-13.
1994: Koonin E V
Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120.
Nucleic acids research 1994;22(13):2476-8.
1994: Mushegian A R; Koonin E V
Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity.
Protein science : a publication of the Protein Society 1994;3(7):1081-8.
1994: Tatusov R L; Koonin E V
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: Karasev A V; Nikolaeva O V; Koonin E V; Gumpf D J; Garnsey S M
Screening of the closterovirus genome by degenerate primer-mediated polymerase chain reaction.
The Journal of general virology 1994;75 ( Pt 6)():1415-22.
1994: Koonin E V; Bork P; Sander C
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: Koonin E V
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: Koonin E V; Rudd K E
A conserved domain in putative bacterial and bacteriophage transglycosylases.
Trends in biochemical sciences 1994;19(3):106-7.
1994: Koonin E V; Bork P; Sander C
Yeast chromosome III: new gene functions.
The EMBO journal 1994;13(3):493-503.
1994: Koonin E V
Conserved sequence pattern in a wide variety of phosphoesterases.
Protein science : a publication of the Protein Society 1994;3(2):356-8.
1994: Agranovsky A A; Koonin E V; Boyko V P; Maiss E; Frötschl R; Lunina N A; Atabekov J G
Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease.
Virology 1994;198(1):311-24.
1993: Koonin E V; Rudd K E
SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases.
Nucleic acids research 1993;21(23):5519.
1993: Senkevich T G; Muravnik G L; Pozdnyakov S G; Chizhikov V E; Ryazankina O I; Shchelkunov S N; Koonin E V; Chernos V I
Nucleotide sequence of XhoI O fragment of ectromelia virus DNA reveals significant differences from vaccinia virus.
Virus research 1993;30(1):73-88.
1993: Koonin E V
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: Koonin E V; Senkevich T G
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: Koonin E V
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: Koonin E V; Deutscher M P
RNase T shares conserved sequence motifs with DNA proofreading exonucleases.
Nucleic acids research 1993;21(10):2521-2.
1993: Koonin E V
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: Koonin E V
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: Koonin E V; Senkevich T G; Chernos V I
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: Koonin E V
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: Koonin E V; Dolja V V
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: Mushegian A R; Koonin E V
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: Koonin E V
A new group of putative RNA helicases.
Trends in biochemical sciences 1992;17(12):495-7.
1992: Koonin E V
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: Boyko V P; Karasev A V; Agranovsky A A; Koonin E V; Dolja V V
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: Choi T J; Kuwata S; Koonin E V; Heaton L A; Jackson A O
Structure of the L (polymerase) protein gene of sonchus yellow net virus.
Virology 1992;189(1):31-9.
1992: Koonin E V; Senkevich T G; Chernos V I
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: Ilyina T V; Gorbalenya A E; Koonin E V
Organization and evolution of bacterial and bacteriophage primase-helicase systems.
Journal of molecular evolution 1992;34(4):351-7.
1992: Koonin E V
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: Koonin E V; Senkevich T G
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: Koonin E V; Senkevich T G
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: Koonin E V
Archaebacterial virus SSV1 encodes a putative DnaA-like protein.
Nucleic acids research 1992;20(5):1143.
1992: Koonin E V; Gorbalenya A E
An insect picornavirus may have genome organization similar to that of caliciviruses.
FEBS letters 1992;297(1-2):81-6.
1991: Verchot J; Koonin E V; Carrington J C
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: Koonin E V; Choi G H; Nuss D L; Shapira R; Carrington J C
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: Koonin E V; Mushegian A R; Ryabov E V; Dolja V V
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: Dolja V V; Boyko V P; Agranovsky A A; Koonin E V
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: Koonin E V
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: Koonin E V; Boyko V P; Dolja V V
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: Agranovsky A A; Boyko V P; Karasev A V; Koonin E V; Dolja V V
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: Agranovsky A A; Boyko V P; Karasev A V; Lunina N A; Koonin E V; Dolja V V
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: Koonin E V; Gorbalenya A E; Chumakov K M
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.

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