Published in Biol Direct on November 27, 2007
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eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res (2009) 4.55
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A (2010) 4.12
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
A unique cell division machinery in the Archaea. Proc Natl Acad Sci U S A (2008) 2.58
Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res (2014) 2.37
Autotrophic carbon fixation in archaea. Nat Rev Microbiol (2010) 2.36
A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet (2008) 2.28
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A (2008) 2.16
Computational methods for Gene Orthology inference. Brief Bioinform (2011) 2.16
Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J (2009) 2.13
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res (2010) 2.00
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The deep archaeal roots of eukaryotes. Mol Biol Evol (2008) 1.90
Phylogenomics of prokaryotic ribosomal proteins. PLoS One (2012) 1.82
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct (2008) 1.78
Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol Direct (2013) 1.75
The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One (2010) 1.71
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct (2012) 1.66
The modern concept of the procaryote. J Bacteriol (2009) 1.64
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol (2008) 1.60
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol (2012) 1.59
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct (2009) 1.58
Evolution of diverse cell division and vesicle formation systems in Archaea. Nat Rev Microbiol (2010) 1.55
Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol (2009) 1.54
The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res (2011) 1.43
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol (2010) 1.40
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol (2008) 1.39
Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev (2014) 1.31
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res (2008) 1.30
Evolutionary primacy of sodium bioenergetics. Biol Direct (2008) 1.23
The evolution of the cytoskeleton. J Cell Biol (2011) 1.22
Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics (2014) 1.18
Autotrophic carbon dioxide assimilation in Thermoproteales revisited. J Bacteriol (2009) 1.17
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J Bacteriol (2012) 1.15
Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship. PLoS One (2011) 1.14
The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem (2011) 1.14
Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J Biol Chem (2009) 1.14
A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya. Biol Direct (2008) 1.13
Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol (2012) 1.11
The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb Perspect Biol (2014) 1.08
The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics (2009) 1.07
Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Genome Biol Evol (2014) 1.03
The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes. Biol Direct (2012) 1.00
Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis. Archaea (2010) 0.97
Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14. Nucleic Acids Res (2011) 0.96
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PLoS One (2011) 0.95
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales. Life (Basel) (2015) 0.95
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions. BMC Genomics (2009) 0.94
Extension of the COG and arCOG databases by amino acid and nucleotide sequences. BMC Bioinformatics (2008) 0.93
Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles (2014) 0.92
The core and unique proteins of haloarchaea. BMC Genomics (2012) 0.91
Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales. Proc Natl Acad Sci U S A (2011) 0.90
Protein Ser/Thr/Tyr phosphorylation in the Archaea. J Biol Chem (2014) 0.89
Characterization of a zinc-containing alcohol dehydrogenase with stereoselectivity from the hyperthermophilic archaeon Thermococcus guaymasensis. J Bacteriol (2011) 0.89
Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? Philos Trans R Soc Lond B Biol Sci (2015) 0.87
Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions. BMC Genomics (2010) 0.86
Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences. Extremophiles (2011) 0.85
MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. BMC Evol Biol (2014) 0.85
Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs. Appl Environ Microbiol (2015) 0.84
Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase. RNA (2014) 0.84
Archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in Sulfolobus acidocaldarius. Mol Cell Proteomics (2013) 0.84
Phylogenomic reconstruction of archaeal fatty acid metabolism. Environ Microbiol (2014) 0.84
Replication-biased genome organisation in the crenarchaeon Sulfolobus. BMC Genomics (2010) 0.83
Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. Structure (2011) 0.83
ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs. BMC Bioinformatics (2012) 0.83
Immunoproteomic identification of immunodominant antigens independent of the time of infection in Brucella abortus 2308-challenged cattle. Vet Res (2015) 0.82
The human postsynaptic density shares conserved elements with proteomes of unicellular eukaryotes and prokaryotes. Front Neurosci (2011) 0.82
Close encounters of the third domain: the emerging genomic view of archaeal diversity and evolution. Archaea (2013) 0.82
GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes. Front Microbiol (2017) 0.82
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PLoS One (2011) 0.81
The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon. BMC Genomics (2012) 0.81
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS One (2014) 0.81
Purine biosynthesis in archaea: variations on a theme. Biol Direct (2011) 0.80
Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Nucleic Acids Res (2009) 0.80
Exploring the evolution of protein function in Archaea. BMC Evol Biol (2012) 0.80
Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics. Mol Cell Proteomics (2016) 0.79
Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association. J Biol (2009) 0.78
Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods. J Virol (2016) 0.78
OMICS in ecology: systems level analyses of Halobacterium salinarum reveal large-scale temperature-mediated changes and a requirement of CctA for thermotolerance. OMICS (2013) 0.77
Assigning a function to a conserved archaeal metallo-β-lactamase from Haloferax volcanii. Extremophiles (2012) 0.75
Application of Subspace Clustering in DNA Sequence Analysis. J Comput Biol (2015) 0.75
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The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
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CRISPR provides acquired resistance against viruses in prokaryotes. Science (2007) 29.74
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Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol (1997) 12.21
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
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Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res (1999) 7.39
The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A (2001) 7.00
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Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A (2000) 5.87
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Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol (1996) 5.50
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res (2001) 5.37
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eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res (2007) 4.84
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. BMC Evol Biol (2003) 4.70
Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol (2001) 4.59
The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res (2002) 4.58
The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature (2000) 4.42
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The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A (2003) 4.36
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The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72
Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res (2005) 3.68
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Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res (2001) 2.99
A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet (2002) 2.97
Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci U S A (2002) 2.95
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An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol (2003) 2.75
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75
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The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity. BMC Genomics (2006) 2.48
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A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
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Selection for short introns in highly expressed genes. Nat Genet (2002) 4.04
Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res (2003) 3.90
Genome trees and the tree of life. Trends Genet (2002) 3.79
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol (2003) 3.72
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55
'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res (2004) 3.50
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct (2006) 3.18
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct (2009) 3.17
Introns and the origin of nucleus-cytosol compartmentalization. Nature (2006) 3.16
One-component systems dominate signal transduction in prokaryotes. Trends Microbiol (2005) 3.09
No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol (2003) 3.07
A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem (2008) 3.00
A universal trend of amino acid gain and loss in protein evolution. Nature (2005) 2.81
Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol (2004) 2.78
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol (2008) 2.74
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol (2009) 2.66
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle (2004) 2.65
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res (2004) 2.62
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A (2009) 2.52
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
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Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res (2004) 2.42
New dimensions of the virus world discovered through metagenomics. Trends Microbiol (2009) 2.41
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet (2004) 2.40
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res (2013) 2.35
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Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol (2002) 2.24
Complete pathway for protein disulfide bond formation encoded by poxviruses. Proc Natl Acad Sci U S A (2002) 2.19
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Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. J Mol Biol (2005) 2.14
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