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Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation.

Berthon J, Cortez D, Forterre P.

Genome Biol. 2008 Apr 9;9(4):R71. [Epub ahead of print]

PMID: 18400081 [PubMed - as supplied by publisher]

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]

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.

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Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

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Genome Res. 2001 Mar;11(3):356-72.

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An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences.

Brochier C, Forterre P, Gribaldo S.

BMC Evol Biol. 2005 Jun 2;5(1):36.

PMID: 15932645 [PubMed - indexed for MEDLINE]

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Predicted highly expressed genes in archaeal genomes.

Karlin S, Mrázek J, Ma J, Brocchieri L.

Proc Natl Acad Sci U S A. 2005 May 17;102(20):7303-8. Epub 2005 May 9.

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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.

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Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics.

Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve JN, et al.

J Bacteriol. 1997 Nov;179(22):7135-55.

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The genome of fowlpox virus.

Afonso CL, Tulman ER, Lu Z, Zsak L, Kutish GF, Rock DL.

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Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach.

Koonin EV, Wolf YI, Aravind L.

Genome Res. 2001 Feb;11(2):240-52.