Published in Genome Res on July 01, 2002
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14
Sequence and structural analysis of BTB domain proteins. Genome Biol (2005) 3.88
Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science (2010) 3.70
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91
Protein family expansions and biological complexity. PLoS Comput Biol (2006) 2.69
The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol (2006) 2.58
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct (2007) 2.53
Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res (2005) 2.50
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A (2009) 2.50
Adaptive evolution in zinc finger transcription factors. PLoS Genet (2009) 2.35
Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biol (2007) 2.19
Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol (2008) 2.14
Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol (2004) 1.95
Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera). Genome Res (2006) 1.92
The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. Genome Biol (2003) 1.91
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res (2008) 1.90
Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol Biol (2002) 1.86
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res (2005) 1.77
Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish. Genome Biol (2007) 1.74
PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol (2007) 1.74
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol (2011) 1.72
Comparative analysis of apicomplexa and genomic diversity in eukaryotes. Genome Res (2004) 1.71
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol Biol (2005) 1.63
Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res (2003) 1.63
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res (2006) 1.62
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56
Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. BMC Genomics (2003) 1.56
Molecular cloning, expression, and structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing metalloenzyme. Proc Natl Acad Sci U S A (2005) 1.56
Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis. MBio (2012) 1.53
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol (2010) 1.53
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS One (2012) 1.47
Regulatory hotspots in the malaria parasite genome dictate transcriptional variation. PLoS Biol (2008) 1.47
Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res (2004) 1.42
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Comparative genomics of Archaea: how much have we learned in six years, and what's next? Genome Biol (2003) 1.38
Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. BMC Evol Biol (2007) 1.32
Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biol (2008) 1.32
Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes. J Mol Evol (2005) 1.31
Extensive functional diversification of the Populus glutathione S-transferase supergene family. Plant Cell (2009) 1.29
Pectin activation of MAP kinase and gene expression is WAK2 dependent. Plant J (2009) 1.29
Phylogenetic analysis of plant basic helix-loop-helix proteins. J Mol Evol (2003) 1.26
Protein structure and evolutionary history determine sequence space topology. Genome Res (2005) 1.22
Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. J Struct Biol (2008) 1.19
Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biol (2002) 1.18
cuticleDB: a relational database of Arthropod cuticular proteins. BMC Bioinformatics (2004) 1.16
Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: the class II cytokine receptors and their ligands in mammals and fish. BMC Genomics (2003) 1.15
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct (2013) 1.14
Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals. PLoS One (2009) 1.09
Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex. BMC Genomics (2009) 1.09
The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification. BMC Evol Biol (2008) 1.06
Genomic expansion and clustering of ZAD-containing C2H2 zinc-finger genes in Drosophila. EMBO Rep (2002) 1.05
The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. PLoS Genet (2013) 1.05
Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol (2008) 1.04
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? Genome Biol (2004) 1.03
Phylogenetic analysis of Ciona intestinalis gene superfamilies supports the hypothesis of successive gene expansions. J Mol Evol (2004) 1.02
Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. BMC Genomics (2015) 0.99
Domain architecture evolution of pattern-recognition receptors. Immunogenetics (2010) 0.99
Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. BMC Evol Biol (2004) 0.99
Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens. BMC Genomics (2015) 0.98
Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. BMC Genomics (2008) 0.97
Novel eukaryotic enzymes modifying cell-surface biopolymers. Biol Direct (2010) 0.96
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Nucleic Acids Res (2009) 0.95
Tandemly arrayed genes in vertebrate genomes. Comp Funct Genomics (2008) 0.95
The phylogenetic distribution of non-CTCF insulator proteins is limited to insects and reveals that BEAF-32 is Drosophila lineage specific. J Mol Evol (2009) 0.95
Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes. BMC Genomics (2007) 0.95
A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response. Funct Integr Genomics (2008) 0.93
Chalcone isomerase family and fold: no longer unique to plants. Protein Sci (2004) 0.92
Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol (2010) 0.92
Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions. Genome Biol (2009) 0.92
Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments. BMC Genomics (2014) 0.91
Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi. PLoS Genet (2013) 0.89
Analysis of the Drosophila melanogaster testes transcriptome reveals coordinate regulation of paralogous genes. Genetics (2008) 0.89
Origin, evolution and classification of type-3 copper proteins: lineage-specific gene expansions and losses across the Metazoa. BMC Evol Biol (2013) 0.89
The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes. J Mol Evol (2006) 0.88
The inflammasomes in health and disease: from genetics to molecular mechanisms of autoinflammation and beyond. Cell Mol Immunol (2011) 0.88
Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis. Mol Genet Genomics (2009) 0.87
Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining. Genome Biol Evol (2012) 0.87
A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses. DNA Res (2009) 0.87
Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae. Genome Res (2014) 0.86
Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus. BMC Evol Biol (2010) 0.86
Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha. BMC Genomics (2013) 0.86
Gene family level comparative analysis of gene expression in mammals validates the ortholog conjecture. Genome Biol Evol (2014) 0.85
Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae). PLoS One (2013) 0.84
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How much does the amphioxus genome represent the ancestor of chordates? Brief Funct Genomics (2012) 0.84
A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages. Genome Biol Evol (2013) 0.84
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Female Anopheles gambiae antennae: increased transcript accumulation of the mosquito-specific odorant-binding-protein OBP2. Parasit Vectors (2012) 0.81
Genus-Wide Comparative Genome Analyses of Colletotrichum Species Reveal Specific Gene Family Losses and Gains during Adaptation to Specific Infection Lifestyles. Genome Biol Evol (2016) 0.81
Functional annotation of novel lineage-specific genes using co-expression and promoter analysis. BMC Genomics (2010) 0.80
Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function. BMC Evol Biol (2011) 0.80
Mago Nashi, Tsunagi/Y14, and Ranshi form a complex that influences oocyte differentiation in Drosophila melanogaster. Dev Biol (2010) 0.80
Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain. Front Plant Sci (2015) 0.80
An atlas of the speed of copy number changes in animal gene families and its implications. PLoS One (2009) 0.79
Gene duplication, lineage-specific expansion, and subfunctionalization in the MADF-BESS family patterns the Drosophila wing hinge. Genetics (2013) 0.79
Comparative genomics reveals molecular features unique to the songbird lineage. BMC Genomics (2014) 0.79
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