Published in Genome Res on June 01, 2001
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol (2004) 7.98
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res (2005) 3.68
Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea (2005) 1.83
PipeAlign: A new toolkit for protein family analysis. Nucleic Acids Res (2003) 1.78
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69
Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res (2002) 1.58
Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J Bacteriol (2006) 1.57
Insertion sequence diversity in archaea. Microbiol Mol Biol Rev (2007) 1.41
Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins. RNA (2002) 1.35
Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol (2002) 1.26
The impact of extremophiles on structural genomics (and vice versa). Extremophiles (2007) 1.11
Decoding the genomic tree of life. Proc Natl Acad Sci U S A (2005) 1.11
Genome sequencing of a genetically tractable Pyrococcus furiosus strain reveals a highly dynamic genome. J Bacteriol (2012) 1.10
Evolutionary analysis by whole-genome comparisons. J Bacteriol (2002) 1.05
Comparative genomic hybridizations of Entamoeba strains reveal unique genetic fingerprints that correlate with virulence. Eukaryot Cell (2005) 1.00
Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis. Appl Environ Microbiol (2004) 0.97
Analysis of genes that encode DtxR-like transcriptional regulators in pathogenic and saprophytic corynebacterial species. Infect Immun (2004) 0.97
Prediction of novel archaeal enzymes from sequence-derived features. Protein Sci (2002) 0.95
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions. BMC Genomics (2009) 0.94
Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment. J Bacteriol (2005) 0.93
The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. BMC Evol Biol (2008) 0.93
Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol (2011) 0.92
A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei. Archaea (2004) 0.88
Comparative genomics reveals birth and death of fragile regions in mammalian evolution. Genome Biol (2010) 0.87
A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res (2002) 0.85
Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638. Curr Microbiol (2011) 0.78
Structural basis of substrate selectivity of E. coli prolidase. PLoS One (2014) 0.77
Cloning, purification, crystallization and preliminary crystallographic analysis of a penicillin-binding protein homologue from Pyrococcus abyssi. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.77
Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific. Front Microbiol (2015) 0.76
Recombinant expression library of Pyrococcus furiosus constructed by high-throughput cloning: a useful tool for functional and structural genomics. Front Microbiol (2015) 0.76
Cloning, purification and crystallization of a Walker-type Pyrococcus abyssi ATPase family member. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.75
Adaptive evolution of genes of archaea belonging to the genus Pyrococcus associated with adaptation to life under high-pressure conditions. Dokl Biochem Biophys (2009) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
A genomic perspective on protein families. Science (1997) 50.51
Distinguishing homologous from analogous proteins. Syst Zool (1970) 25.10
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature (1999) 19.34
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol (1997) 17.52
Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol (1995) 14.60
Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol (1997) 12.21
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res (2000) 8.69
Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol Microbiol (1997) 8.69
Genome phylogeny based on gene content. Nat Genet (1999) 8.12
Measuring genome evolution. Proc Natl Acad Sci U S A (1998) 6.97
Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res (1998) 6.79
Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat Genet (1999) 5.81
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res (2000) 5.70
Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol (2000) 5.06
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet (1998) 4.10
Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev (1997) 3.94
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res (1999) 3.62
Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res (1989) 3.35
The impact of comparative genomics on our understanding of evolution. Cell (2000) 3.25
Non-orthologous gene displacement. Trends Genet (1996) 3.12
Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics (1996) 3.00
Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science (2000) 2.64
An archaeal genomic signature. Proc Natl Acad Sci U S A (2000) 2.53
The genomic tree as revealed from whole proteome comparisons. Genome Res (1999) 2.47
Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics (1995) 2.32
Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol (1997) 2.29
Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res (1997) 2.28
Rearrangement of the bacterial chromosome: forbidden inversions. Science (1988) 2.26
What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol Microbiol (1998) 2.26
Testing for equality of evolutionary rates. Genetics (1992) 2.25
Insights into the evolutionary process of genome degradation. Curr Opin Genet Dev (1999) 2.25
Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology (1991) 2.12
Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles (1998) 2.10
From complete genomes to measures of substitution rate variability within and between proteins. Genome Res (2000) 2.09
Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. Genetics (1999) 1.94
Universal protein families and the functional content of the last universal common ancestor. J Mol Evol (1999) 1.77
Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup. J Mol Evol (2000) 1.66
Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr Opin Genet Dev (1997) 1.55
Sensitivity of the relative-rate test to taxonomic sampling. Mol Biol Evol (1998) 1.54
Where is the root of the universal tree of life? Bioessays (1999) 1.53
Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J Bacteriol (1996) 1.41
Transfer RNAs and pathogenicity islands. Trends Biochem Sci (1999) 1.39
SSV1-encoded site-specific recombination system in Sulfolobus shibatae. Mol Gen Genet (1993) 1.39
Archaeal genomics: do archaea have a mixed heritage? Curr Biol (1998) 1.38
Hyperrecombination in the terminus region of the Escherichia coli chromosome: possible relation to nucleoid organization. J Bacteriol (1994) 1.38
Deletions at stalled replication forks occur by two different pathways. EMBO J (1997) 1.37
Conserved gene clusters in bacterial genomes provide further support for the primacy of RNA. J Mol Evol (1997) 1.36
Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence. Genetics (1991) 1.33
Sulfolobus genome: from genomics to biology. Curr Opin Microbiol (1998) 1.17
DNA repair systems in archaea: mementos from the last universal common ancestor? J Mol Evol (1999) 1.13
Archaebacterial genomes: eubacterial form and eukaryotic content. Curr Opin Genet Dev (1994) 1.11
Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? Trends Genet (1999) 1.05
The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor. Mol Biol Evol (1998) 1.03
Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium. J Bacteriol (1994) 1.02
Phylogenetic invariants for genome rearrangements. J Comput Biol (1999) 0.97
Mycoplasma pneumoniae and Mycoplasma genitalium: a comparison of two closely related bacterial species. Curr Opin Microbiol (1998) 0.92
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
A gene map of the human genome. Science (1996) 14.32
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics (1999) 12.64
A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res (1999) 12.56
A physical map of 30,000 human genes. Science (1998) 12.43
A physical map of the human genome. Nature (2001) 12.39
Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature (1990) 9.21
An attempt to unify the structure of polymerases. Protein Eng (1990) 7.93
Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature (2001) 7.53
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res (2001) 6.67
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res (2000) 5.70
Cutting edge: inflammatory responses can be triggered by TREM-1, a novel receptor expressed on neutrophils and monocytes. J Immunol (2000) 5.37
Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science (1991) 4.87
The ovalbumin gene family: structure of the X gene and evolution of duplicated split genes. Cell (1980) 4.14
Walking along the rabies genome: is the large G-L intergenic region a remnant gene? Proc Natl Acad Sci U S A (1986) 3.49
Towards a reliable objective function for multiple sequence alignments. J Mol Biol (2001) 3.07
Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene (2001) 2.88
Rift Valley fever virus L segment: correction of the sequence and possible functional role of newly identified regions conserved in RNA-dependent polymerases. J Gen Virol (1994) 2.84
RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics (2003) 2.79
The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res (2001) 2.75
Mutations in CGI-58, the gene encoding a new protein of the esterase/lipase/thioesterase subfamily, in Chanarin-Dorfman syndrome. Am J Hum Genet (2001) 2.72
A human homologue of the Drosophila eyes absent gene underlies branchio-oto-renal (BOR) syndrome and identifies a novel gene family. Nat Genet (1997) 2.68
Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science (2000) 2.64
Crystal structure of yeast tRNAAsp. Nature (1980) 2.61
Yeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase. Nature (1993) 2.57
Isolation and characterization of cDNA clones for human skeletal muscle alpha actin. Nucleic Acids Res (1983) 2.45
Sequence and structure of D-glyceraldehyde 3-phosphate dehydrogenase from Bacillus stearothermophilus. Nature (1977) 2.42
Regional localization on the human X chromosome and polymorphism of the coagulation factor IX gene (hemophilia B locus). Proc Natl Acad Sci U S A (1984) 2.23
Completion of the rabies virus genome sequence determination: highly conserved domains among the L (polymerase) proteins of unsegmented negative-strand RNA viruses. Virology (1988) 2.02
The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J (1994) 1.99
A DNA fragment from the human X chromosome short arm which detects a partially homologous sequence on the Y chromosomes long arm. Nucleic Acids Res (1984) 1.93
Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step. EMBO J (1999) 1.88
The Genexpress Index: a resource for gene discovery and the genic map of the human genome. Genome Res (1995) 1.83
A summary of recent findings on birth outcomes and developmental effects of prenatal ETS, PAH, and pesticide exposures. Neurotoxicology (2005) 1.81
Additional polymorphisms at marker loci D9S5 and D9S15 generate extended haplotypes in linkage disequilibrium with Friedreich ataxia. Proc Natl Acad Sci U S A (1990) 1.78
Characterization of the NPHP1 locus: mutational mechanism involved in deletions in familial juvenile nephronophthisis. Am J Hum Genet (2000) 1.73
Genetic screening for hemophilia A (classic hemophilia) with a polymorphic DNA probe. N Engl J Med (1985) 1.67
The chicken dystrophin cDNA: striking conservation of the C-terminal coding and 3' untranslated regions between man and chicken. EMBO J (1988) 1.65
Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family. Cell (1998) 1.63
Negative side-effects of retention sutures for abdominal wound closure. A prospective randomised study. Eur J Surg (2000) 1.62
Search for supersymmetry using final states with one lepton, jets, and missing transverse momentum with the ATLAS detector in √s=7 TeV pp collisions. Phys Rev Lett (2011) 1.60
Clustering of mutations responsible for branchio-oto-renal (BOR) syndrome in the eyes absent homologous region (eyaHR) of EYA1. Hum Mol Genet (1997) 1.59
Comprehensive analysis of a large genomic sequence at the putative B-cell chronic lymphocytic leukaemia (B-CLL) tumour suppresser gene locus. Mutat Res (2001) 1.59
Detection of proopiomelanocortin-derived antigens in normal and pathologic human skin. J Lab Clin Med (1993) 1.58
Secator: a program for inferring protein subfamilies from phylogenetic trees. Mol Biol Evol (2001) 1.57
Head and neck squamous cell carcinoma transcriptome analysis by comprehensive validated differential display. Oncogene (2006) 1.56
Primary structure of leader RNA and nucleoprotein genes of the rabies genome: segmented homology with VSV. Nucleic Acids Res (1986) 1.53
Mutations in the gene encoding SLURP-1 in Mal de Meleda. Hum Mol Genet (2001) 1.50
Genetic mapping of the human X chromosome: linkage analysis of the q26-q28 region that includes the fragile X locus and isolation of expressed sequences. Cold Spring Harb Symp Quant Biol (1986) 1.47
The human TFIID components TAF(II)135 and TAF(II)20 and the yeast SAGA components ADA1 and TAF(II)68 heterodimerize to form histone-like pairs. Mol Cell Biol (2000) 1.45
A novel gene that encodes a protein with a putative src homology 3 domain is a candidate gene for familial juvenile nephronophthisis. Hum Mol Genet (1997) 1.44
A new recurrent and specific cryptic translocation, t(5;14)(q35;q32), is associated with expression of the Hox11L2 gene in T acute lymphoblastic leukemia. Leukemia (2001) 1.43
Observation of a centrality-dependent dijet asymmetry in lead-lead collisions at sqrt[S(NN)] =2.76 TeV with the ATLAS detector at the LHC. Phys Rev Lett (2010) 1.41
First steps towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high biomedical value. Acta Crystallogr D Biol Crystallogr (2006) 1.40
Measurement of dijet azimuthal decorrelations in pp collisions at sqrt(s)=7 TeV. Phys Rev Lett (2011) 1.39
Structure and function of poly(ADP-ribose) polymerase. Mol Cell Biochem (1994) 1.38
Regulation of pyruvate dehydrogenase complex synthesis in Escherichia coli K 12. Identification of the inducing metabolite. Eur J Biochem (1970) 1.35
Determination of the strange-quark density of the proton from ATLAS measurements of the W→ℓν and Z→ℓℓ cross sections. Phys Rev Lett (2012) 1.34
Genetic analysis of the fragile-X mental retardation syndrome with two flanking polymorphic DNA markers. Proc Natl Acad Sci U S A (1986) 1.34
GOAnno: GO annotation based on multiple alignment. Bioinformatics (2005) 1.34
Identification of 28 novel mutations in the Bardet-Biedl syndrome genes: the burden of private mutations in an extensively heterogeneous disease. Hum Genet (2010) 1.33
The TBP-like factor: an alternative transcription factor in metazoa? Trends Biochem Sci (1999) 1.33
Search for new particles in two-jet final states in 7 TeV proton-proton collisions with the ATLAS detector at the LHC. Phys Rev Lett (2010) 1.32
Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J (1998) 1.31
A 195-kb cosmid walk encompassing the human Xq28 color vision pigment genes. Genomics (1990) 1.28
The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism. EMBO J (2001) 1.28
Laparoscopic cholecystectomy: technical performance, safety and patient's benefit. Endoscopy (1992) 1.27
Observation of associated near-side and away-side long-range correlations in sqrt[s(NN)]=5.02 TeV proton-lead collisions with the ATLAS detector. Phys Rev Lett (2013) 1.27
The ovalbumin gene family. The 5' end region of the X and Y genes. J Mol Biol (1982) 1.25
Expression and site-directed mutagenesis of the catalytic domain of human poly(ADP-ribose)polymerase in Escherichia coli. Lysine 893 is critical for activity. J Biol Chem (1990) 1.22
Fatal nonbacterial pneumonia associated with Adenovirus type 4. Occurrence in an adult. JAMA (1967) 1.20
Search for dark matter candidates and large extra dimensions in events with a photon and missing transverse momentum in pp collision data at sqrt[s]=7 TeV with the ATLAS detector. Phys Rev Lett (2013) 1.19
The 'PINIT' motif, of a newly identified conserved domain of the PIAS protein family, is essential for nuclear retention of PIAS3L. FEBS Lett (2003) 1.18
Sudden infant death. Normal cardiac habituation and poor autonomic control. N Engl J Med (1974) 1.18
The ovalbumin gene family: complete sequence and structure of the Y gene. Nucleic Acids Res (1982) 1.16
An informative polymorphism detectable by polymerase chain reaction at the 3' end of the dystrophin gene. Hum Genet (1990) 1.16
Do white matter changes contribute to the subsequent development of dementia in patients with mild cognitive impairment? A longitudinal study. Int J Geriatr Psychiatry (2000) 1.15
Identification of potential active-site residues in the human poly(ADP-ribose) polymerase. J Biol Chem (1993) 1.15
Search for a supersymmetric partner to the top quark in final states with jets and missing transverse momentum at sqrt[s] = 7 TeV with the ATLAS detector. Phys Rev Lett (2012) 1.13
Isolated dystrophin molecules as seen by electron microscopy. Proc Natl Acad Sci U S A (1990) 1.13
Nonradioactive assay for new microsatellite polymorphisms at the 5' end of the dystrophin gene, and estimation of intragenic recombination. Am J Hum Genet (1991) 1.13
Ballast: blast post-processing based on locally conserved segments. Bioinformatics (2000) 1.13
Homologies between X and Y chromosomes detected by DNA probes: localisation and evolution. Nucleic Acids Res (1985) 1.13
Mu-opioid receptor activation induces transcriptional plasticity in the central extended amygdala. Eur J Neurosci (2008) 1.12
Repetitive satellite-like sequences are present within or upstream from 3 avian protein-coding genes. Nucleic Acids Res (1983) 1.12
Crystal structure of a prokaryotic aspartyl tRNA-synthetase. EMBO J (1994) 1.11
The transmembrane adaptor protein TRIM regulates T cell receptor (TCR) expression and TCR-mediated signaling via an association with the TCR zeta chain. J Exp Med (2001) 1.11
Rapid PCR analysis of the St14 (DXS52) VNTR. Nucleic Acids Res (1991) 1.10
Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase. J Mol Biol (1994) 1.10
Yeast transfer RNAasp: a new high-resolution x-ray diffracting crystal form of a transfer RNA. J Mol Biol (1977) 1.09
The disruption of the rod-derived cone viability gene leads to photoreceptor dysfunction and susceptibility to oxidative stress. Cell Death Differ (2010) 1.08
SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr (2006) 1.08
The structure of cyclin H: common mode of kinase activation and specific features. EMBO J (1997) 1.08