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The source of laterally transferred genes in bacterial genomes.

Daubin V, Lerat E, Perrière G.

Genome Biol. 2003;4(9):R57. Epub 2003 Aug 21.PMID: 12952536 [PubMed - indexed for MEDLINE]Related articlesFree article

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution.

Andersson JO, Sjögren AM, Horner DS, Murphy CA, Dyal PL, Svärd SG, Logsdon JM Jr, Ragan MA, Hirt RP, Roger AJ.

BMC Genomics. 2007 Feb 14;8:51.PMID: 17298675 [PubMed - indexed for MEDLINE]Related articlesFree article

Compositional correlation studies among the three different codon positions in 12 bacterial genomes.

Majumdar S, Gupta SK, Sundararajan VS, Ghosh TC.

Biochem Biophys Res Commun. 1999 Dec 9;266(1):66-71.PMID: 10581166 [PubMed - indexed for MEDLINE]Related articles

Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis.

Guo FB, Yuan JB.

DNA Res. 2009 Apr;16(2):91-104. Epub 2009 Feb 15.PMID: 19221094 [PubMed - indexed for MEDLINE]Related articlesFree article

Speciation in Chlamydia: genomewide phylogenetic analyses identified a reliable set of acquired genes.

Ortutay C, Gáspári Z, Tóth G, Jáger E, Vida G, Orosz L, Vellai T.

J Mol Evol. 2003 Dec;57(6):672-80.PMID: 14745536 [PubMed - indexed for MEDLINE]Related articles

Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses.

Monier A, Claverie JM, Ogata H.

BMC Genomics. 2007 Dec 10;8:456.PMID: 18070355 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Limitations of compositional approach to identifying horizontally transferred genes.

Wang B.

J Mol Evol. 2001 Sep;53(3):244-50.PMID: 11523011 [PubMed - indexed for MEDLINE]Related articles

Comparative DNA analysis across diverse genomes.

Karlin S, Campbell AM, Mrázek J.

Annu Rev Genet. 1998;32:185-225. Review.PMID: 9928479 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages.

Chen LL, Zhang CT.

Biochem Biophys Res Commun. 2003 Jun 20;306(1):310-7.PMID: 12788106 [PubMed - indexed for MEDLINE]Related articles

Examining bacterial species under the specter of gene transfer and exchange.

Ochman H, Lerat E, Daubin V.

Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6595-9. Epub 2005 Apr 25. Review.PMID: 15851673 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.

Mau B, Glasner JD, Darling AE, Perna NT.

Genome Biol. 2006;7(5):R44. Epub 2006 May 31.PMID: 16737554 [PubMed - indexed for MEDLINE]Related articlesFree article

Amelioration of bacterial genomes: rates of change and exchange.

Lawrence JG, Ochman H.

J Mol Evol. 1997 Apr;44(4):383-97.PMID: 9089078 [PubMed - indexed for MEDLINE]Related articles

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes.

Guindon S, Perrière G.

Mol Biol Evol. 2001 Sep;18(9):1838-40. No abstract available. PMID: 11504864 [PubMed - indexed for MEDLINE]Related articlesFree article

A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.

Cortez D, Forterre P, Gribaldo S.

Genome Biol. 2009;10(6):R65. Epub 2009 Jun 16.PMID: 19531232 [PubMed - indexed for MEDLINE]Related articlesFree article

Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis.

Marri PR, Bannantine JP, Paustian ML, Golding GB.

Can J Microbiol. 2006 Jun;52(6):560-9.PMID: 16788724 [PubMed - indexed for MEDLINE]Related articles

Synonymous codon usage is subject to selection in thermophilic bacteria.

Lynn DJ, Singer GA, Hickey DA.

Nucleic Acids Res. 2002 Oct 1;30(19):4272-7.PMID: 12364606 [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

HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes.

Garcia-Vallve S, Guzman E, Montero MA, Romeu A.

Nucleic Acids Res. 2003 Jan 1;31(1):187-9.PMID: 12519978 [PubMed - indexed for MEDLINE]Related articlesFree article