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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
:R7
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PubMed Central articles that cite the above article:
1.
Prevalence of intron gain over intron loss in the evolution of paralogous gene families.
Babenko VN, Rogozin IB, Mekhedov SL, Koonin EV
Nucleic Acids Res
2004,
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Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.
Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV
J Bacteriol
2004 Oct,
186
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Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved.
Babenko VN, Krylov DM
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2004,
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Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes.
Martinez MJ, Roy S, Archuletta AB, Wentzell PD, Anna-Arriola SS, Rodriguez AL, Aragon AD, Quiñones GA, Allen C, Werner-Washburne M
Mol Biol Cell
2004 Dec,
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The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics.
Roth C, Betts MJ, Steffansson P, Saelensminde G, Liberles DA
Nucleic Acids Res
2005 Jan 1,
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Exploring the plant transcriptome through phylogenetic profiling.
Vandepoele K, Van de Peer Y
Plant Physiol
2005 Jan,
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Genome-wide annotation and expression profiling of cell cycle regulatory genes in Chlamydomonas reinhardtii.
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Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.
Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV
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Evolutionary change of the numbers of homeobox genes in bilateral animals.
Nam J, Nei M
Mol Biol Evol
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Unifying measures of gene function and evolution.
Wolf YI, Carmel L, Koonin EV
Proc Biol Sci
2006 Jun 22,
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Assessing performance of orthology detection strategies applied to eukaryotic genomes.
Chen F, Mackey AJ, Vermunt JK, Roos DS
PLoS ONE
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The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV
Proc Natl Acad Sci U S A
2007 May 1,
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The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase.
Yu Z, Genest PA, ter Riet B, Sweeney K, DiPaolo C, Kieft R, Christodoulou E, Perrakis A, Simmons JM, Hausinger RP, van Luenen HG, Rigden DJ, Sabatini R, Borst P
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Evolutionarily conserved genes preferentially accumulate introns.
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Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.
Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR
Insect Mol Biol
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Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes.
Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, Ast G
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Evolution of protein domain promiscuity in eukaryotes.
Basu MK, Carmel L, Rogozin IB, Koonin EV
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18.
Analysis of the Drosophila melanogaster testes transcriptome reveals coordinate regulation of paralogous genes.
Mikhaylova LM, Nguyen K, Nurminsky DI
Genetics
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