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Yuri Wolf

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Evolution, Molecular

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Genomics

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TOP 3
Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Comparative genomics of defense systems in archaea and bacteria.
David Managadze; Igor B Rogozin; Svetlana A Shabalina; Yuri I Wolf; Alexander E Lobkovsky; Eugene V Koonin
The vast, conserved mammalian lincRNome.
Pere Puigbò; Yuri I Wolf; Eugene V Koonin
Seeing the Tree of Life behind the phylogenetic forest.

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All Publications

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 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: Pere Puigbò; Yuri I Wolf; Eugene V Koonin
Seeing the Tree of Life behind the phylogenetic forest.
BMC biology 2013;11():46.
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.
2012: Michael Galperin; Sergei L Mekhedov; Pere Puigbo; Sergey Smirnov; Yuri I Wolf; Daniel J Rigden
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes.
Environmental microbiology 2012;14(11):2870-90.
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: 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: 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: Natalya Yutin; Eugene V Koonin; Pere Puigbò; Yuri I Wolf
Phylogenomics of prokaryotic ribosomal proteins.
PloS one 2012;7(5):e36972.
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.
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: 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; 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: 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.
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: 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: Yuri I Wolf; Anastasia Nikolskaya; Joshua L Cherry; Cécile Viboud; Eugene Koonin; David Lipman
Projection of seasonal influenza severity from sequence and serological data.
PLoS currents 2010;2():RRN1200.
2010: Eugene V Koonin; Yuri I Wolf
The common ancestry of life.
Biology direct 2010;5():64.
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: 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: 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.
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: Joshua L Cherry; David Lipman; Anastasia Nikolskaya; Yuri I Wolf
Evolutionary dynamics of N-glycosylation sites of influenza virus hemagglutinin.
PLoS currents 2009;1():RRN1001.
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: Eugene V Koonin; Yuri I Wolf
Is evolution Darwinian or/and Lamarckian?
Biology direct 2009;4():42.
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: 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: 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: 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: 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: 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: 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: Armen Y Mulkidjanian; Michael Galperin; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Evolutionary primacy of sodium bioenergetics.
Biology direct 2008;3():13.
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: 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: 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: 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: 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.
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: 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: Yuri I Wolf
Coping with the quantitative genomics 'elephant': the correlation between the gene dispensability and evolution rate.
Trends in genetics : TIG 2006;22(7):354-7.
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: 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: 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.
2005: Anna R Panchenko; Yuri I Wolf; Larisa A Panchenko; Thomas Madej
Evolutionary plasticity of protein families: coupling between sequence and structure variation.
Proteins 2005;61(3):535-44.
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: 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: 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.
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: 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: 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: 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: 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: 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: 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: 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: 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: 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.
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: 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: 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: 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: I King Jordan; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
Microevolutionary genomics of bacteria.
Theoretical population biology 2002;61(4):435-47.
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: 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: 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: 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: 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: 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: Fyodor A Kondrashov; Igor Rogozin; Yuri I Wolf; Eugene V Koonin
Selection in the evolution of gene duplications.
Genome biology 2002;3(2):RESEARCH0008.
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: 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: 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: 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: 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: 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: 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: 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: 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.
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: 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: 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: 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.
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: Kira S Makarova; Yuri I Wolf; Owen R White; KW Minton; Michael J Daly
Short repeats and IS elements in the extremely radiation-resistant bacterium Deinococcus radiodurans and comparison to other bacterial species.
Research in microbiology 1999;150(9-10):711-24.
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: 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: 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; Roman L Tatusov; Yuri I Wolf; D R Walker; E V Koonin
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles.
Trends in genetics : TIG 1998;14(11):442-4.