Published in Nucleic Acids Res on January 01, 2000
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The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res (2001) 43.17
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OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03
TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res (2001) 20.84
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STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
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Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A (2001) 9.40
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Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol (2001) 6.46
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FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res (2002) 4.92
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75
Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev (2013) 4.69
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Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol (2001) 4.59
ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins. Nucleic Acids Res (2001) 4.47
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
iProClass: an integrated, comprehensive and annotated protein classification database. Nucleic Acids Res (2001) 4.33
Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics (2011) 4.15
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A (2007) 4.04
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SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55
Benchmarking ortholog identification methods using functional genomics data. Genome Biol (2006) 3.54
Bacterial signal transduction network in a genomic perspective. Environ Microbiol (2004) 3.45
The complete genome and proteome of Mycoplasma mobile. Genome Res (2004) 3.36
Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res (2002) 3.26
Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell (2013) 3.26
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. Nucleic Acids Res (2001) 3.26
Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol (2005) 3.14
Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res (2001) 3.10
Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources? BMC Genomics (2009) 3.08
Protein Information Resource: a community resource for expert annotation of protein data. Nucleic Acids Res (2001) 3.01
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A (2008) 2.97
Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc Natl Acad Sci U S A (2001) 2.95
Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell (2002) 2.93
Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature (2010) 2.93
Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res (2001) 2.92
Functional classification using phylogenomic inference. PLoS Comput Biol (2006) 2.88
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res (2000) 2.79
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature (2009) 2.72
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res (2008) 2.71
Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res (2001) 2.65
Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet (2013) 2.63
Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. Proc Natl Acad Sci U S A (2003) 2.61
Systematic identification of functional orthologs based on protein network comparison. Genome Res (2006) 2.47
Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res (2014) 2.37
The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability. Proc Natl Acad Sci U S A (2003) 2.37
Proteomic analysis of the spore coats of Bacillus subtilis and Bacillus anthracis. J Bacteriol (2003) 2.34
Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics (2007) 2.29
Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One (2007) 2.28
An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet (2010) 2.28
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol (2006) 2.27
Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. BMC Biol (2009) 2.24
Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci U S A (2000) 2.24
Bambus 2: scaffolding metagenomes. Bioinformatics (2011) 2.24
Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res (2002) 2.24
Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida. FEMS Microbiol Rev (2011) 2.24
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Res (2001) 2.23
Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol Mol Biol Rev (2004) 2.19
Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J Bacteriol (2009) 2.15
The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A (2006) 2.11
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. Genome Biol (2001) 2.10
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res (2009) 2.09
Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J Bacteriol (2006) 2.02
Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens. Proc Natl Acad Sci U S A (2007) 2.00
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res (2003) 1.98
Bacterial phylogeny structures soil resistomes across habitats. Nature (2014) 1.98
Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. J Bacteriol (2003) 1.97
Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons. Microbiol Mol Biol Rev (2001) 1.95
Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics (2008) 1.94
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations. EMBO Rep (2002) 1.94
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol Direct (2009) 1.92
The deep archaeal roots of eukaryotes. Mol Biol Evol (2008) 1.90
TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89
Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA (2003) 1.89
Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol Biol (2002) 1.86
Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags. Proc Natl Acad Sci U S A (2000) 1.84
Amino acid addition to Vibrio cholerae LPS establishes a link between surface remodeling in gram-positive and gram-negative bacteria. Proc Natl Acad Sci U S A (2012) 1.83
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics (2009) 1.80
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct (2008) 1.78
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res (2005) 1.77
Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect Immun (2001) 1.77
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J Bacteriol (2005) 1.77
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