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The evolution of domain-content in bacterial genomes.

Molina N, van Nimwegen E.

Biol Direct. 2008 Dec 11;3:51.PMID: 19077245 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Birth and death of protein domains: a simple model of evolution explains power law behavior.

Karev GP, Wolf YI, Rzhetsky AY, Berezovskaya FS, Koonin EV.

BMC Evol Biol. 2002 Oct 14;2(1):18.PMID: 12379152 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Protein domains and architectural innovation in plant-associated Proteobacteria.

Studholme DJ, Downie JA, Preston GM.

BMC Genomics. 2005 Feb 16;6(1):17.PMID: 15715905 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution.

Wolf MY, Wolf YI, Koonin EV.

Biol Direct. 2008 Oct 7;3:40.PMID: 18840284 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4.

Chen K, Roberts E, Luthey-Schulten Z.

BMC Evol Biol. 2009 Jul 29;9:179.PMID: 19640295 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution.

Rausch C, Hoof I, Weber T, Wohlleben W, Huson DH.

BMC Evol Biol. 2007 May 16;7:78.PMID: 17506888 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Universal features in the genome-level evolution of protein domains.

Cosentino Lagomarsino M, Sellerio AL, Heijning PD, Bassetti B.

Genome Biol. 2009;10(1):R12. Epub 2009 Jan 30.PMID: 19183449 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Protein domain organisation: adding order.

Kummerfeld SK, Teichmann SA.

BMC Bioinformatics. 2009 Jan 29;10:39.PMID: 19178743 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Uncovering rate variation of lateral gene transfer during bacterial genome evolution.

Hao W, Golding GB.

BMC Genomics. 2008 May 20;9:235. Erratum in: BMC Genomics. 2008(9):556. PMID: 18492275 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria.

Belda E, Moya A, Silva FJ.

Mol Biol Evol. 2005 Jun;22(6):1456-67. Epub 2005 Mar 16.PMID: 15772379 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes.

Pagel M, Meade A, Scott D.

BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S16.PMID: 17288574 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?

Karev GP, Wolf YI, Koonin EV.

Bioinformatics. 2003 Oct 12;19(15):1889-900.PMID: 14555621 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.

Jordan IK, Kondrashov FA, Rogozin IB, Tatusov RL, Wolf YI, Koonin EV.

Genome Biol. 2001;2(12):RESEARCH0053. Epub 2001 Nov 20.PMID: 11790256 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

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 citations

Prokaryotic phylogenies inferred from protein structural domains.

Deeds EJ, Hennessey H, Shakhnovich EI.

Genome Res. 2005 Mar;15(3):393-402.PMID: 15741510 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins.

Axelsen JB, Yan KK, Maslov S.

Biol Direct. 2007 Nov 26;2:32.PMID: 18039386 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Modeling the evolution of protein domain architectures using maximum parsimony.

Fong JH, Geer LY, Panchenko AR, Bryant SH.

J Mol Biol. 2007 Feb 9;366(1):307-15. Epub 2006 Nov 10.PMID: 17166515 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences.

Wagner A, de la Chaux N.

Mol Genet Genomics. 2008 Nov;280(5):397-408. Epub 2008 Aug 28.PMID: 18751731 [PubMed - indexed for MEDLINE]Related citations

Patterns of bacterial gene movement.

Hao W, Golding GB.

Mol Biol Evol. 2004 Jul;21(7):1294-307. Epub 2004 Apr 28.PMID: 15115802 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria.

Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D.

Biol Direct. 2009 Apr 10;4:13.PMID: 19361336 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations