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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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.

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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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Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.

Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV.

Genome Biol. 2003;4(9):R55. Epub 2003 Aug 29.

PMID: 12952534 [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.

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Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes.

Coenye T, Vandamme P.

FEMS Microbiol Lett. 2005 Jan 1;242(1):117-26.

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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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Evolution of gene fusions: horizontal transfer versus independent events.

Yanai I, Wolf YI, Koonin EV.

Genome Biol. 2002;3(5):research0024. Epub 2002 Apr 26.

PMID: 12049665 [PubMed - indexed for MEDLINE]

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Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications.

Siegel N, Hoegg S, Salzburger W, Braasch I, Meyer A.

BMC Genomics. 2007 Sep 6;8:312.

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Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.

Wolf YI, Aravind L, Grishin NV, Koonin EV.

Genome Res. 1999 Aug;9(8):689-710.

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Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR.

Owen GA, Pascoe B, Kallifidas D, Paget MS.

J Bacteriol. 2007 Jun;189(11):4078-86. Epub 2007 Mar 30.

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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.

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The balance of driving forces during genome evolution in prokaryotes.

Kunin V, Ouzounis CA.

Genome Res. 2003 Jul;13(7):1589-94.

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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.

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Lineage-specific gene expansions in bacterial and archaeal genomes.

Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV.

Genome Res. 2001 Apr;11(4):555-65.

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Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract.

Nicolas P, Bessières P, Ehrlich SD, Maguin E, van de Guchte M.

BMC Evol Biol. 2007 Aug 20;7:141.

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The evolutionary duplication and probable demise of an endodermal GATA factor in Caenorhabditis elegans.

Fukushige T, Goszczynski B, Tian H, McGhee JD.

Genetics. 2003 Oct;165(2):575-88.

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The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.

Koonin EV, Makarova KS, Rogozin IB, Davidovic L, Letellier MC, Pellegrini L.

Genome Biol. 2003;4(3):R19. Epub 2003 Feb 28.

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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.

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Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer.

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