PubMed

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

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).

Natale DA, Shankavaram UT, Galperin MY, Wolf YI, Aravind L, Koonin EV.

Genome Biol. 2000;1(5):RESEARCH0009. Epub 2000 Nov 6.PMID: 11178258 [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 COG database: a tool for genome-scale analysis of protein functions and evolution.

Tatusov RL, Galperin MY, Natale DA, Koonin EV.

Nucleic Acids Res. 2000 Jan 1;28(1):33-6.PMID: 10592175 [PubMed - indexed for MEDLINE]Related articlesFree article

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 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

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

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV.

Genome Res. 1999 Jul;9(7):608-28.PMID: 10413400 [PubMed - indexed for MEDLINE]Related articlesFree article

The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV.

Nucleic Acids Res. 2001 Jan 1;29(1):22-8.PMID: 11125040 [PubMed - indexed for MEDLINE]Related articlesFree article

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

The origins of modern proteomes.

Kurland CG, Canbäck B, Berg OG.

Biochimie. 2007 Dec;89(12):1454-63. Epub 2007 Sep 15.PMID: 17949885 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data.

Lemoine F, Lespinet O, Labedan B.

BMC Evol Biol. 2007 Nov 29;7:237.PMID: 18047665 [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

Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.

Brochier C, Forterre P, Gribaldo S.

Genome Biol. 2004;5(3):R17. Epub 2004 Feb 26.PMID: 15003120 [PubMed - indexed for MEDLINE]Related articlesFree article

PHOG: a database of supergenomes built from proteome complements.

Merkeev IV, Novichkov PS, Mironov AA.

BMC Evol Biol. 2006 Jun 22;6:52.PMID: 16792803 [PubMed - indexed for MEDLINE]Related articlesFree article

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Remm M, Storm CE, Sonnhammer EL.

J Mol Biol. 2001 Dec 14;314(5):1041-52.PMID: 11743721 [PubMed - indexed for MEDLINE]Related articles

FUNYBASE: a FUNgal phYlogenomic dataBASE.

Marthey S, Aguileta G, Rodolphe F, Gendrault A, Giraud T, Fournier E, Lopez-Villavicencio M, Gautier A, Lebrun MH, Chiapello H.

BMC Bioinformatics. 2008 Oct 27;9:456.PMID: 18954438 [PubMed - indexed for MEDLINE]Related articlesFree article

Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".

Koonin EV, Makarova KS, Elkins JG.

Biol Direct. 2007 Dec 14;2:38.PMID: 18081935 [PubMed - indexed for MEDLINE]Related articlesFree article

Archaeal phylogeny based on ribosomal proteins.

Matte-Tailliez O, Brochier C, Forterre P, Philippe H.

Mol Biol Evol. 2002 May;19(5):631-9.PMID: 11961097 [PubMed - indexed for MEDLINE]Related articlesFree article