PubMed

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]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.

Ge F, Wang LS, Kim J.

PLoS Biol. 2005 Oct;3(10):e316. Epub 2005 Aug 30.PMID: 16122348 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.

Podell S, Gaasterland T, Allen EE.

BMC Bioinformatics. 2008 Oct 7;9:419.PMID: 18840280 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article

Genome trees and the tree of life.

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

Trends Genet. 2002 Sep;18(9):472-9. Review.PMID: 12175808 [PubMed - indexed for MEDLINE]Related articles

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]Related articles

A likelihood framework to measure horizontal gene transfer.

Linz S, Radtke A, von Haeseler A.

Mol Biol Evol. 2007 Jun;24(6):1312-9. Epub 2007 Mar 20. Erratum in: Mol Biol Evol. 2007 Jul;24(7):1576. PMID: 17374878 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions.

Than C, Ruths D, Innan H, Nakhleh L.

J Comput Biol. 2007 May;14(4):517-35.PMID: 17572027 [PubMed - indexed for MEDLINE]Related articles

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]Related articles

Identification and categorization of horizontally transferred genes in prokaryotic genomes.

Shi SY, Cai XH, Ding DF.

Acta Biochim Biophys Sin (Shanghai). 2005 Aug;37(8):561-6.PMID: 16077904 [PubMed - indexed for MEDLINE]Related articlesFree article

A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective.

Ouzounis CA, Kunin V, Darzentas N, Goldovsky L.

Res Microbiol. 2006 Jan-Feb;157(1):57-68. Epub 2005 Dec 19.PMID: 16431085 [PubMed - indexed for MEDLINE]Related articles

Decoding the genomic tree of life.

Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA.

Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6608-13. Epub 2005 Apr 25.PMID: 15851667 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article