Log on / register
Feedback | Support | My details
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
[Full text] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]


printer friendly 
to  [Help]

PubMed Central articles that cite the above article:

1.
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, 186:6575-85
 [PubMed Central] [PubMed] [Related articles]
2.
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
Nucleic Acids Res 2004, 32:5029-35
 [PubMed Central] [PubMed] [Related articles]
3.
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, 33:D495-7
 [PubMed Central] [PubMed] [Related articles]
4.
Genome-wide annotation and expression profiling of cell cycle regulatory genes in Chlamydomonas reinhardtii.
Bisova K, Krylov DM, Umen JG
Plant Physiol 2005 Feb, 137:475-91
 [PubMed Central] [PubMed] [Related articles]
5.
Evolutionary change of the numbers of homeobox genes in bilateral animals.
Nam J, Nei M
Mol Biol Evol 2005 Dec, 22:2386-94
 [PubMed Central] [PubMed] [Related articles]
6.
Assessing performance of orthology detection strategies applied to eukaryotic genomes.
Chen F, Mackey AJ, Vermunt JK, Roos DS
PLoS One 2007, 2:e383
 [PubMed Central] [PubMed] [Related articles]
7.
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, 104:7705-10
 [PubMed Central] [PubMed] [Related articles]
8.
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
Nucleic Acids Res 2007, 35:2107-15
 [PubMed Central] [PubMed] [Related articles]
9.
Evolutionarily conserved genes preferentially accumulate introns.
Carmel L, Rogozin IB, Wolf YI, Koonin EV
Genome Res 2007 Jul, 17:1045-50
 [PubMed Central] [PubMed] [Related articles]
10.
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 2006 Oct, 15:657-86
 [PubMed Central] [PubMed] [Related articles]
11.
Evolution of protein domain promiscuity in eukaryotes.
Basu MK, Carmel L, Rogozin IB, Koonin EV
Genome Res 2008 Mar, 18:449-61
 [PubMed Central] [PubMed] [Related articles]
12.
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, 32:3724-33
 [PubMed Central] [PubMed] [Related articles]
13.
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, 15:5295-305
 [PubMed Central] [PubMed] [Related articles]
14.
Exploring the plant transcriptome through phylogenetic profiling.
Vandepoele K, Van de Peer Y
Plant Physiol 2005 Jan, 137:31-42
 [PubMed Central] [PubMed] [Related articles]
15.
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.
Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV
Nucleic Acids Res 2005, 33:4626-38
 [PubMed Central] [PubMed] [Related articles]
16.
Unifying measures of gene function and evolution.
Wolf YI, Carmel L, Koonin EV
Proc Biol Sci 2006 Jun 22, 273:1507-15
 [PubMed Central] [PubMed] [Related articles]
17.
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
Genome Res 2008 Jan, 18:88-103
 [PubMed Central] [PubMed] [Related articles]
18.
A whole-genome RNAi Screen for C. elegans miRNA pathway genes.
Parry DH, Xu J, Ruvkun G
Curr Biol 2007 Dec 4, 17:2013-22
 [PubMed Central] [PubMed] [Related articles]
19.
Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species.
Martens C, Vandepoele K, Van de Peer Y
Proc Natl Acad Sci U S A 2008 Mar 4, 105:3427-32
 [PubMed Central] [PubMed] [Related articles]
20.
Analysis of the Drosophila melanogaster testes transcriptome reveals coordinate regulation of paralogous genes.
Mikhaylova LM, Nguyen K, Nurminsky DI
Genetics 2008 May, 179:305-15
 [PubMed Central] [PubMed] [Related articles]
21.
Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function.
Mazumder R, Vasudevan S
PLoS Comput Biol 2008, 4:e1000151
 [PubMed Central] [PubMed] [Related articles]
22.
Dissecting colony development of Neurospora crassa using mRNA profiling and comparative genomics approaches.
Kasuga T, Glass NL
Eukaryot Cell 2008 Sep, 7:1549-64
 [PubMed Central] [PubMed] [Related articles]
23.
Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library.
Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, Yamaguchi-Shinozaki K, Shinozaki K
DNA Res 2008 Dec, 15:333-46
 [PubMed Central] [PubMed] [Related articles]
24.
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.
Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmström J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO
PLoS Biol 2009 Mar 3, 7:e48
 [PubMed Central] [PubMed] [Related articles]
25.
*** Unable to retrieve article 19260763 ***

 [PubMed Central] [PubMed] [Related articles]
26.
Darwinian evolution in the light of genomics.
Koonin EV
Nucleic Acids Res 2009 Mar, 37:1011-34
 [PubMed Central] [PubMed] [Related articles]
27.
Inaugural Article: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages.
Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ
Proc Natl Acad Sci U S A 2009 May 5, 106:7273-80
 [PubMed Central] [PubMed] [Related articles]
28.
Linking fold, function and phylogeny: a comparative genomics view on protein (domain) evolution.
Te Velthuis AJ, Bagowski CP
Curr Genomics 2008 Apr, 9:88-96
 [PubMed Central] [PubMed] [Related articles]
29.
Relationship between phylogenetic distribution and genomic features in Neurospora crassa.
Kasuga T, Mannhaupt G, Glass NL
PLoS One 2009, 4:e5286
 [PubMed Central] [PubMed] [Related articles]

This article is also cited by 27 articles in BioMed Central


You can also check ISI Web of Science for additional citations (subscription required)
  
printer friendly 
to  [Help]
Terms and Conditions Privacy statement Information for advertisers Jobs at BMC Contact us
© 1999-2009 BioMed Central Ltd unless otherwise stated. Part of Springer Science+Business Media.