Published in Nature on March 02, 2006
The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A (2007) 4.96
Crystal structure of a self-spliced group II intron. Science (2008) 4.66
The energetics of genome complexity. Nature (2010) 4.58
The ancient Virus World and evolution of cells. Biol Direct (2006) 3.06
Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet (2010) 2.70
Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev (2012) 2.65
An archaeal origin of eukaryotes supports only two primary domains of life. Nature (2013) 2.31
The tree of one percent. Genome Biol (2006) 2.23
Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb Perspect Biol (2011) 2.22
Prokaryotic evolution and the tree of life are two different things. Biol Direct (2009) 2.17
Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol (2008) 2.15
Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res (2007) 2.06
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol (2010) 1.95
Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana. Plant Physiol (2008) 1.95
The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol (2010) 1.92
Darwinian evolution in the light of genomics. Nucleic Acids Res (2009) 1.92
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
RNA catalyses nuclear pre-mRNA splicing. Nature (2013) 1.86
Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol (2007) 1.82
Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays (2011) 1.76
Origin and evolution of spliceosomal introns. Biol Direct (2012) 1.65
Mechanisms used for genomic proliferation by thermophilic group II introns. PLoS Biol (2010) 1.62
Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci (2006) 1.59
Critical association of ncRNA with introns. Nucleic Acids Res (2010) 1.54
The origins of phagocytosis and eukaryogenesis. Biol Direct (2009) 1.49
Evolution of genome architecture. Int J Biochem Cell Biol (2008) 1.48
Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor. Genome Biol Evol (2016) 1.43
Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc Natl Acad Sci U S A (2007) 1.43
The function of introns. Front Genet (2012) 1.42
Patterns of intron gain and conservation in eukaryotic genes. BMC Evol Biol (2007) 1.42
The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct (2008) 1.40
Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit Rev Biochem Mol Biol (2013) 1.39
Energetics and genetics across the prokaryote-eukaryote divide. Biol Direct (2011) 1.36
Genome reduction as the dominant mode of evolution. Bioessays (2013) 1.36
The ribonome: a dominant force in co-ordinating gene expression. Biol Cell (2009) 1.35
Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PLoS One (2010) 1.33
A virocentric perspective on the evolution of life. Curr Opin Virol (2013) 1.29
The early evolution of lipid membranes and the three domains of life. Nat Rev Microbiol (2012) 1.28
Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct (2010) 1.26
Wide diversity in structure and expression profiles among members of the Caenorhabditis elegans globin protein family. BMC Genomics (2007) 1.26
Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat. J Cell Biol (2011) 1.25
The Biological Big Bang model for the major transitions in evolution. Biol Direct (2007) 1.25
Structural basis for exon recognition by a group II intron. Nat Struct Mol Biol (2008) 1.24
Bioenergetic constraints on the evolution of complex life. Cold Spring Harb Perspect Biol (2014) 1.21
The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon. Proc Natl Acad Sci U S A (2006) 1.21
Endosymbiotic theories for eukaryote origin. Philos Trans R Soc Lond B Biol Sci (2015) 1.19
Rab protein evolution and the history of the eukaryotic endomembrane system. Cell Mol Life Sci (2010) 1.15
Evolutionary origins of metabolic compartmentalization in eukaryotes. Philos Trans R Soc Lond B Biol Sci (2010) 1.14
An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol Evol (2012) 1.14
Towards a postmodern synthesis of evolutionary biology. Cell Cycle (2009) 1.11
Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry. Philos Trans R Soc Lond B Biol Sci (2008) 1.11
Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity. Biol Direct (2009) 1.09
The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb Perspect Biol (2014) 1.08
Intron-dominated genomes of early ancestors of eukaryotes. J Hered (2009) 1.07
A rapid ribosome profiling method elucidates chloroplast ribosome behavior in vivo. Plant Cell (2013) 1.07
Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry. Genes Dev (2010) 1.07
Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective. Nat Rev Genet (2009) 1.07
Early evolution without a tree of life. Biol Direct (2011) 1.05
The new biology: beyond the Modern Synthesis. Biol Direct (2007) 1.03
The case for junk DNA. PLoS Genet (2014) 1.00
Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome. Proc Natl Acad Sci U S A (2007) 0.99
The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I. Mol Cell Biol (2012) 0.99
Identifying the mechanisms of intron gain: progress and trends. Biol Direct (2012) 0.98
Intron presence-absence polymorphisms in Daphnia. Mol Biol Evol (2008) 0.98
Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages. Plant Physiol (2013) 0.97
Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria. Proc Natl Acad Sci U S A (2012) 0.95
The common ancestor of archaea and eukarya was not an archaeon. Archaea (2013) 0.95
Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering! Curr Genet (2006) 0.94
The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms. BMC Evol Biol (2010) 0.94
Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PLoS One (2011) 0.93
Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes. Genome Biol Evol (2013) 0.93
An inside-out origin for the eukaryotic cell. BMC Biol (2014) 0.92
Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. Proc Natl Acad Sci U S A (2015) 0.92
Non-coding RNA: what is functional and what is junk? Front Genet (2015) 0.92
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol Direct (2006) 0.92
Phase distribution of spliceosomal introns: implications for intron origin. BMC Evol Biol (2006) 0.92
Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis. Mob DNA (2014) 0.91
Crystal structure of a group II intron in the pre-catalytic state. Nat Struct Mol Biol (2012) 0.91
Evolution of group II introns. Mob DNA (2015) 0.91
Archaeal ancestors of eukaryotes: not so elusive any more. BMC Biol (2015) 0.90
Origin of spliceosomal introns and alternative splicing. Cold Spring Harb Perspect Biol (2014) 0.90
Exaptive origins of regulated mRNA decay in eukaryotes. Bioessays (2016) 0.90
Missing pieces of an ancient puzzle: evolution of the eukaryotic membrane-trafficking system. Cold Spring Harb Perspect Biol (2014) 0.89
The retrohoming of linear group II intron RNAs in Drosophila melanogaster occurs by both DNA ligase 4-dependent and -independent mechanisms. PLoS Genet (2012) 0.89
Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation. Philos Trans R Soc Lond B Biol Sci (2013) 0.89
A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes. Biol Direct (2011) 0.89
Molecular Data are Transforming Hypotheses on the Origin and Diversification of Eukaryotes. Bioscience (2009) 0.89
Uniting sex and eukaryote origins in an emerging oxygenic world. Biol Direct (2010) 0.89
Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core. Proc Natl Acad Sci U S A (2013) 0.88
Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses. Ann N Y Acad Sci (2015) 0.88
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
Protecting exons from deleterious R-loops: a potential advantage of having introns. Biol Direct (2007) 0.87
Evolutionary diversification of the Sm family of RNA-associated proteins. Mol Biol Evol (2008) 0.87
Comparative genomics of proteins involved in RNA nucleocytoplasmic export. BMC Evol Biol (2011) 0.87
Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell. Biol Direct (2008) 0.85
Alternative splicing of a group II intron in a surface layer protein gene in Clostridium tetani. Nucleic Acids Res (2013) 0.85
How retrotransposons shape genome regulation. Curr Opin Genet Dev (2016) 0.85
Linear group II intron RNAs can retrohome in eukaryotes and may use nonhomologous end-joining for cDNA ligation. Proc Natl Acad Sci U S A (2009) 0.85
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Small CRISPR RNAs guide antiviral defense in prokaryotes. Science (2008) 17.79
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature (2004) 12.41
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
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25
Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol (2002) 6.85
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res (2002) 6.08
Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD. Science (2004) 5.88
Selection in the evolution of gene duplications. Genome Biol (2002) 5.58
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95
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
Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res (2006) 4.49
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet (2003) 4.39
The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28
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
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
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
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct (2007) 2.53
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
Evolution and classification of P-loop kinases and related proteins. J Mol Biol (2003) 2.52
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
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
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
Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res (2002) 2.35
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
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
Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol (2008) 2.15
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
Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J (2009) 2.13
The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A (2006) 2.11
Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem (2006) 2.10
STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. J Mol Biol (2004) 2.10
Functional and evolutionary implications of gene orthology. Nat Rev Genet (2013) 2.07
Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res (2007) 2.06
Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol (2006) 2.04
Evolutionary significance of gene expression divergence. Gene (2004) 2.04
Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res (2006) 2.02
Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics (2002) 1.99
Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A (2012) 1.96
The relationship of protein conservation and sequence length. BMC Evol Biol (2002) 1.95
Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana. Plant Physiol (2008) 1.95
Microevolutionary genomics of bacteria. Theor Popul Biol (2002) 1.95
SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. J Mol Microbiol Biotechnol (2002) 1.95
Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol (2004) 1.95
Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res (2010) 1.93
GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep (2006) 1.91
The deep archaeal roots of eukaryotes. Mol Biol Evol (2008) 1.90
Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform (2005) 1.89
Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol Biol (2002) 1.86
Evolutionary genomics of lactic acid bacteria. J Bacteriol (2006) 1.84
Phylogenomics of prokaryotic ribosomal proteins. PLoS One (2012) 1.82
Evolution of protein domain promiscuity in eukaryotes. Genome Res (2008) 1.82
Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res (2013) 1.82
Trends in protein evolution inferred from sequence and structure analysis. Curr Opin Struct Biol (2002) 1.81
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
Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends Genet (2003) 1.80
Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol (2008) 1.79
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
Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays (2011) 1.76
Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes. J Mol Microbiol Biotechnol (2003) 1.76
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
Purifying and directional selection in overlapping prokaryotic genes. Trends Genet (2002) 1.74
Biological applications of the theory of birth-and-death processes. Brief Bioinform (2006) 1.68
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics (2010) 1.67
Conservation versus parallel gains in intron evolution. Nucleic Acids Res (2005) 1.67
Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA. Proteins (2002) 1.67
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
Origin and evolution of spliceosomal introns. Biol Direct (2012) 1.65
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol Biol (2005) 1.63
Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A (2004) 1.62