Published in Nucleic Acids Res on September 01, 1999
Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev (2010) 5.81
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78
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
Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00
The genetic core of the universal ancestor. Genome Res (2003) 3.82
Cell cycle regulation of DNA replication. Annu Rev Genet (2007) 3.80
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56
The ancient Virus World and evolution of cells. Biol Direct (2006) 3.06
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
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res (2005) 2.49
DNA replication in the archaea. Microbiol Mol Biol Rev (2006) 2.17
On the origin of biochemistry at an alkaline hydrothermal vent. Philos Trans R Soc Lond B Biol Sci (2007) 2.15
Darwinian evolution in the light of genomics. Nucleic Acids Res (2009) 1.92
Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc Natl Acad Sci U S A (2006) 1.90
The deep archaeal roots of eukaryotes. Mol Biol Evol (2008) 1.90
The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct (2006) 1.88
Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Struct Biol (2003) 1.80
A bioenergetic basis for membrane divergence in archaea and bacteria. PLoS Biol (2014) 1.72
Three monophyletic superfamilies account for the majority of the known glycosyltransferases. Protein Sci (2003) 1.68
Insertion sequence diversity in archaea. Microbiol Mol Biol Rev (2007) 1.41
The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct (2008) 1.40
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol (2010) 1.40
Identification of short 'eukaryotic' Okazaki fragments synthesized from a prokaryotic replication origin. EMBO Rep (2003) 1.39
Comparative genomics of Archaea: how much have we learned in six years, and what's next? Genome Biol (2003) 1.38
An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Nucleic Acids Res (2007) 1.36
Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol Direct (2009) 1.33
On the origin of cells and viruses: primordial virus world scenario. Ann N Y Acad Sci (2009) 1.29
Mechanisms for initiating cellular DNA replication. Annu Rev Biochem (2013) 1.28
A novel type of replicative enzyme harbouring ATPase, primase and DNA polymerase activity. EMBO J (2003) 1.28
Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol Mol Biol Rev (2014) 1.26
The Biological Big Bang model for the major transitions in evolution. Biol Direct (2007) 1.25
Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res (2009) 1.25
On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol Direct (2007) 1.24
From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. Philos Trans R Soc Lond B Biol Sci (2006) 1.20
Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci (2013) 1.20
Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance. Nucleic Acids Res (2009) 1.17
Protein superfamily evolution and the last universal common ancestor (LUCA). J Mol Evol (2006) 1.17
A cytoprotective perspective on longevity regulation. Trends Cell Biol (2013) 1.15
Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol (2001) 1.11
Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA. Protein Sci (2003) 1.11
An origin-of-life reactor to simulate alkaline hydrothermal vents. J Mol Evol (2014) 1.08
The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb Perspect Biol (2014) 1.08
On the origin of DNA genomes: evolution of the division of labor between template and catalyst in model replicator systems. PLoS Comput Biol (2011) 1.08
Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii. J Bacteriol (2005) 1.07
Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. Biol Direct (2010) 1.07
Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci (2009) 1.07
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct (2009) 1.01
Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis. J Bacteriol (2013) 1.01
Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaea (Cdc6p). Proc Natl Acad Sci U S A (2001) 1.01
Replisome structure and conformational dynamics underlie fork progression past obstacles. Curr Opin Cell Biol (2009) 0.99
Genomic sequence of Spodoptera frugiperda Ascovirus 1a, an enveloped, double-stranded DNA insect virus that manipulates apoptosis for viral reproduction. J Virol (2006) 0.99
Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode. Proc Natl Acad Sci U S A (2009) 0.99
Histone deacetylases in fungi: novel members, new facts. Nucleic Acids Res (2003) 0.98
A broad host range replicon with different requirements for replication initiation in three bacterial species. EMBO J (2001) 0.98
Archaeology of eukaryotic DNA replication. Cold Spring Harb Perspect Biol (2013) 0.98
Optical tweezers experiments resolve distinct modes of DNA-protein binding. Biopolymers (2009) 0.97
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC. BMC Genomics (2012) 0.97
Replisome dynamics and use of DNA trombone loops to bypass replication blocks. Mol Biosyst (2008) 0.95
Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. Nucleic Acids Res (2007) 0.94
Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D. Nucleic Acids Res (2004) 0.92
DNA polymerases BI and D from the hyperthermophilic archaeon Pyrococcus furiosus both bind to proliferating cell nuclear antigen with their C-terminal PIP-box motifs. J Bacteriol (2007) 0.92
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol Direct (2006) 0.92
Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res (2013) 0.91
Three proliferating cell nuclear antigen-like proteins found in the hyperthermophilic archaeon Aeropyrum pernix: interactions with the two DNA polymerases. J Bacteriol (2002) 0.91
An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Syst Biol (2010) 0.91
Activation of the MCM helicase from the thermophilic archaeon, Thermoplasma acidophilum by interactions with GINS and Cdc6-2. Extremophiles (2014) 0.90
Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III alpha subunit. ACS Chem Biol (2008) 0.90
Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales. Proc Natl Acad Sci U S A (2011) 0.90
Crystal structure of the human primase. J Biol Chem (2014) 0.88
The universal tree of life: an update. Front Microbiol (2015) 0.86
Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size. Nucleic Acids Res (2011) 0.86
Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes. Nucleic Acids Res (2015) 0.85
A proposal: Evolution of PCNA's role as a marker of newly replicated DNA. DNA Repair (Amst) (2015) 0.85
The place of RNA in the origin and early evolution of the genetic machinery. Life (Basel) (2014) 0.84
The solution structure of the amino-terminal domain of human DNA polymerase epsilon subunit B is homologous to C-domains of AAA+ proteins. Nucleic Acids Res (2008) 0.84
Cloning and characterization of a family B DNA polymerase from the hyperthermophilic crenarchaeon Pyrobaculum islandicum. J Bacteriol (2000) 0.84
Carl Woese's vision of cellular evolution and the domains of life. RNA Biol (2014) 0.84
Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes? Biol Direct (2006) 0.83
Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin. Front Cell Infect Microbiol (2012) 0.83
Intein Clustering Suggests Functional Importance in Different Domains of Life. Mol Biol Evol (2015) 0.83
The origin of modern terrestrial life. HFSP J (2007) 0.83
RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Nucleic Acids Res (2016) 0.81
The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes. Nucleic Acids Res (2016) 0.81
The GINS complex from the thermophilic archaeon, Thermoplasma acidophilum may function as a homotetramer in DNA replication. Extremophiles (2011) 0.81
Open Questions on the Origin of Eukaryotes. Trends Ecol Evol (2015) 0.80
Modelling evolution on design-by-contract predicts an origin of life through an abiotic double-stranded RNA world. Biol Direct (2007) 0.80
Distribution of DNA replication proteins in Drosophila cells. BMC Cell Biol (2007) 0.80
Mechanisms and regulation of DNA replication initiation in eukaryotes. Crit Rev Biochem Mol Biol (2017) 0.79
The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. Biol Direct (2011) 0.79
Kinetics and fidelity of polymerization by DNA polymerase III from Sulfolobus solfataricus. Biochemistry (2012) 0.79
Systems biology perspectives on minimal and simpler cells. Microbiol Mol Biol Rev (2014) 0.78
Structural Mechanisms of Hexameric Helicase Loading, Assembly, and Unwinding. F1000Res (2016) 0.78
Evolution of replication machines. Crit Rev Biochem Mol Biol (2015) 0.78
The case for an early biological origin of DNA. J Mol Evol (2014) 0.78
The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes. J Mol Evol (2010) 0.78
Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin. PLoS One (2011) 0.77
Mutational analysis of Pyrococcus furiosus replication factor C based on the three-dimensional structure. Extremophiles (2003) 0.77
Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication. Elife (2016) 0.77
A model for the evolution of nucleotide polymerase directionality. PLoS One (2011) 0.77
Theory of the origin, evolution, and nature of life. Life (Basel) (2011) 0.76
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
A genomic perspective on protein families. Science (1997) 50.51
The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res (2000) 49.22
The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res (2001) 43.17
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (2009) 32.97
Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res (1998) 23.87
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A (1994) 18.46
A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J (1997) 15.10
Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science (1998) 13.64
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature (2004) 12.41
BRCA1 protein products ... Functional motifs... Nat Genet (1996) 11.50
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res (1999) 11.30
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science (2000) 10.82
Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res (1989) 10.03
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature (2010) 8.87
Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett (2001) 8.45
Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol (2001) 8.14
Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. Trends Biochem Sci (1998) 8.01
Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science (1999) 8.01
Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect (2012) 7.97
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics (1999) 6.91
Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol (2002) 6.85
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol (2000) 6.50
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol (2001) 6.46
A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A (1996) 6.38
Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (1998) 6.28
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol (1998) 6.22
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol (1999) 5.90
Using the COG database to improve gene recognition in complete genomes. Genetica (2000) 5.80
Cleavage of cohesin by the CD clan protease separin triggers anaphase in yeast. Cell (2000) 5.69
Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science (2004) 5.64
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
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95
Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res (1999) 4.80
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75
Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68
Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol (2001) 4.59
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res (2006) 4.49
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc Natl Acad Sci U S A (1997) 4.40
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol (2001) 4.39
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res (1992) 4.39
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Lett (1989) 4.29
Common origin of four diverse families of large eukaryotic DNA viruses. J Virol (2001) 4.28
The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28
N-terminal domains of putative helicases of flavi- and pestiviruses may be serine proteases. Nucleic Acids Res (1989) 4.27
Identification of paracaspases and metacaspases: two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma. Mol Cell (2000) 4.19
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14
The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci (1998) 4.11
SAP - a putative DNA-binding motif involved in chromosomal organization. Trends Biochem Sci (2000) 4.10
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet (1998) 4.10
The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase. Virology (1991) 4.07
Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol (2000) 4.04
Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol (2000) 3.99
Viral proteins containing the purine NTP-binding sequence pattern. Nucleic Acids Res (1989) 3.96
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science (1998) 3.83
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res (1999) 3.62
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56
Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res (1999) 3.44
Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis. Nucleic Acids Res (1989) 3.38
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
DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res (1999) 3.32
A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett (1990) 3.30
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J Mol Biol (1999) 3.28
Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci U S A (2000) 3.27
Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol (2003) 3.26
The impact of comparative genomics on our understanding of evolution. Cell (2000) 3.25
PAS: a multifunctional domain family comes to light. Curr Biol (1997) 3.20
TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol (2013) 3.18
Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol (2007) 3.14
Non-orthologous gene displacement. Trends Genet (1996) 3.12
Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res (2001) 3.10
Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol (2006) 3.10
A novel superfamily of nucleoside triphosphate-binding motif containing proteins which are probably involved in duplex unwinding in DNA and RNA replication and recombination. FEBS Lett (1988) 3.09
Malaria parasite clag3 genes determine channel-mediated nutrient uptake by infected red blood cells. Cell (2011) 3.06
Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol (2003) 3.02