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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

Identification and investigation of ORFans in the viral world.

Yin Y, Fischer D.

BMC Genomics. 2008 Jan 19;9:24.PMID: 18205946 [PubMed - indexed for MEDLINE]Related articlesFree article

On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.

Yin Y, Fischer D.

BMC Evol Biol. 2006 Aug 16;6:63.PMID: 16914045 [PubMed - indexed for MEDLINE]Related articlesFree article

Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.

Bocs S, Danchin A, Médigue C.

BMC Bioinformatics. 2002;3:5. Epub 2002 Feb 5.PMID: 11879526 [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

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes.

Zhu H, Hu GQ, Yang YF, Wang J, She ZS.

BMC Bioinformatics. 2007 Mar 16;8:97.PMID: 17367537 [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

Retroids in archaea: phylogeny and lateral origins.

Rest JS, Mindell DP.

Mol Biol Evol. 2003 Jul;20(7):1134-42. Epub 2003 May 30.PMID: 12777534 [PubMed - indexed for MEDLINE]Related articlesFree article

Use of artificial genomes in assessing methods for atypical gene detection.

Azad RK, Lawrence JG.

PLoS Comput Biol. 2005 Nov;1(6):e56. Epub 2005 Nov 11.PMID: 16292353 [PubMed - indexed for MEDLINE]Related articlesFree article

Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches.

Olendzenski L, Liu L, Zhaxybayeva O, Murphey R, Shin DG, Gogarten JP.

J Mol Evol. 2000 Dec;51(6):587-99.PMID: 11116332 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA.

Nature. 2009 Dec 24;462(7276):1056-60.PMID: 20033048 [PubMed - indexed for MEDLINE]Related articles

Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli.

Daubin V, Ochman H.

Genome Res. 2004 Jun;14(6):1036-42.PMID: 15173110 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

Zhou F, Olman V, Xu Y.

BMC Genomics. 2008 Jan 24;9:36.PMID: 18218090 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of singleton ORFans in fully sequenced microbial genomes.

Siew N, Fischer D.

Proteins. 2003 Nov 1;53(2):241-51.PMID: 14517975 [PubMed - indexed for MEDLINE]Related articles

Archaeal integrative genetic elements and their impact on genome evolution.

She Q, Brügger K, Chen L.

Res Microbiol. 2002 Jul-Aug;153(6):325-32. Review.PMID: 12234006 [PubMed - indexed for MEDLINE]Related articles

New findings on evolution of metal homeostasis genes: evidence from comparative genome analysis of bacteria and archaea.

Coombs JM, Barkay T.

Appl Environ Microbiol. 2005 Nov;71(11):7083-91.PMID: 16269744 [PubMed - indexed for MEDLINE]Related articlesFree article

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Besemer J, Lomsadze A, Borodovsky M.

Nucleic Acids Res. 2001 Jun 15;29(12):2607-18.PMID: 11410670 [PubMed - indexed for MEDLINE]Related articlesFree article

Status of genome projects for nonpathogenic bacteria and archaea.

Nelson KE, Paulsen IT, Heidelberg JF, Fraser CM.

Nat Biotechnol. 2000 Oct;18(10):1049-54. Review.PMID: 11017041 [PubMed - indexed for MEDLINE]Related articles