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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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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]
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]
Interkingdom gene fusions.
Wolf YI, Kondrashov AS, Koonin EV.
Genome Biol. 2000;1(6):RESEARCH0013. Epub 2000 Dec 4.
PMID: 11178267 [PubMed - indexed for MEDLINE]
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]
Genomes in flux: the evolution of archaeal and proteobacterial gene content.
Snel B, Bork P, Huynen MA.
Genome Res. 2002 Jan;12(1):17-25.
PMID: 11779827 [PubMed - indexed for MEDLINE]
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A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV.
Nucleic Acids Res. 2002 Jan 15;30(2):482-96.
PMID: 11788711 [PubMed - indexed for MEDLINE]
The balance of driving forces during genome evolution in prokaryotes.
Kunin V, Ouzounis CA.
Genome Res. 2003 Jul;13(7):1589-94.
PMID: 12840037 [PubMed - indexed for MEDLINE]
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]
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]
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.
Leipe DD, Koonin EV, Aravind L.
J Mol Biol. 2004 Oct 8;343(1):1-28. Review.
PMID: 15381417 [PubMed - indexed for MEDLINE]
The ring of life provides evidence for a genome fusion origin of eukaryotes.
Rivera MC, Lake JA.
Nature. 2004 Sep 9;431(7005):152-5.
PMID: 15356622 [PubMed - indexed for MEDLINE]
Horizontal gene transfer in bacterial and archaeal complete genomes.
Garcia-Vallvé S, Romeu A, Palau J.
Genome Res. 2000 Nov;10(11):1719-25.
PMID: 11076857 [PubMed - indexed for MEDLINE]
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.
PMID: 12620104 [PubMed - indexed for MEDLINE]
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.
PMID: 10447505 [PubMed - indexed for MEDLINE]
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.
Biol Direct. 2007 Nov 27;2:33.
PMID: 18042280 [PubMed - indexed for MEDLINE]
Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria.
Nesbo CL, L'Haridon S, Stetter KO, Doolittle WF.
Mol Biol Evol. 2001 Mar;18(3):362-75.
PMID: 11230537 [PubMed - indexed for MEDLINE]
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns.
Glazko GV, Mushegian AR.
Genome Biol. 2004;5(5):R32. Epub 2004 Apr 27.
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Ancient origin of the tryptophan operon and the dynamics of evolutionary change.
Xie G, Keyhani NO, Bonner CA, Jensen RA.
Microbiol Mol Biol Rev. 2003 Sep;67(3):303-42, table of contents. Review.
PMID: 12966138 [PubMed - indexed for MEDLINE]
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]