A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.

Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

Genome Biol. 2004;5(2):R7. Epub 2004 Jan 15.

PMID: 14759257 [PubMed - indexed for MEDLINE]

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The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11.

PMID: 12969510 [PubMed - indexed for MEDLINE]

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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.

Mirkin BG, Fenner TI, Galperin MY, Koonin EV.

BMC Evol Biol. 2003 Jan 6;3:2. Epub 2003 Jan 6.

PMID: 12515582 [PubMed - indexed for MEDLINE]

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Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved.

Babenko VN, Krylov DM.

Nucleic Acids Res. 2004 Sep 24;32(17):5029-35. Print 2004.

PMID: 15448184 [PubMed - indexed for MEDLINE]

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The role of lineage-specific gene family expansion in the evolution of eukaryotes.

Lespinet O, Wolf YI, Koonin EV, Aravind L.

Genome Res. 2002 Jul;12(7):1048-59.

PMID: 12097341 [PubMed - indexed for MEDLINE]

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Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.

Krylov DM, Wolf YI, Rogozin IB, Koonin EV.

Genome Res. 2003 Oct;13(10):2229-35.

PMID: 14525925 [PubMed - indexed for MEDLINE]

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Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV.

Genome Res. 2001 Mar;11(3):356-72.

PMID: 11230160 [PubMed - indexed for MEDLINE]

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Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.

Iyer LM, Balaji S, Koonin EV, Aravind L.

Virus Res. 2006 Apr;117(1):156-84. Epub 2006 Feb 21. Review.

PMID: 16494962 [PubMed - indexed for MEDLINE]

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

Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV.

Nucleic Acids Res. 2005 Aug 16;33(14):4626-38. Print 2005.

PMID: 16106042 [PubMed - indexed for MEDLINE]

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Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals.

Danchin EG, Gouret P, Pontarotti P.

BMC Evol Biol. 2006 Jan 18;6:5.

PMID: 16420703 [PubMed - indexed for MEDLINE]

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Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases.

Iyer LM, Koonin EV, Aravind L.

BMC Struct Biol. 2003 Jan 28;3:1. Epub 2003 Jan 28.

PMID: 12553882 [PubMed - indexed for MEDLINE]

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Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.

PMID: 11734060 [PubMed - indexed for MEDLINE]

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Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV.

Genome Res. 1999 Jul;9(7):608-28.

PMID: 10413400 [PubMed - indexed for MEDLINE]

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Evolutionary sequence analysis of complete eukaryote genomes.

Blair JE, Shah P, Hedges SB.

BMC Bioinformatics. 2005 Mar 11;6:53.

PMID: 15762985 [PubMed - indexed for MEDLINE]

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Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.

Koonin EV, Mushegian AR, Galperin MY, Walker DR.

Mol Microbiol. 1997 Aug;25(4):619-37.

PMID: 9379893 [PubMed - indexed for MEDLINE]

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Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP.

BMC Genomics. 2008 Aug 27;9:399.

PMID: 18752680 [PubMed - indexed for MEDLINE]

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Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.

Pandey R, Müller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA.

Nucleic Acids Res. 2002 Dec 1;30(23):5036-55.

PMID: 12466527 [PubMed - indexed for MEDLINE]

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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.

Makarova KS, Ponomarev VA, Koonin EV.

Genome Biol. 2001;2(9):RESEARCH 0033. Epub 2001 Aug 30.

PMID: 11574053 [PubMed - indexed for MEDLINE]

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Unique genes in plants: specificities and conserved features throughout evolution.

Armisén D, Lecharny A, Aubourg S.

BMC Evol Biol. 2008 Oct 10;8:280.

PMID: 18847470 [PubMed - indexed for MEDLINE]

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The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH.

PLoS Biol. 2003 Nov;1(2):E45. Epub 2003 Nov 17.

PMID: 14624247 [PubMed - indexed for MEDLINE]

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