Published in BMC Biol on May 19, 2014
An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol (2015) 3.74
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Mol Cell (2015) 1.89
CRISPR-Cas adaptation: insights into the mechanism of action. Nat Rev Microbiol (2016) 1.05
Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery. Front Microbiol (2014) 0.90
The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications. Nucleic Acids Res (2015) 0.88
CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease. Mob DNA (2014) 0.84
Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements. J Virol (2016) 0.83
Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems. Curr Opin Microbiol (2016) 0.82
Viruses and mobile elements as drivers of evolutionary transitions. Philos Trans R Soc Lond B Biol Sci (2016) 0.80
Protecting genome integrity during CRISPR immune adaptation. Nat Struct Mol Biol (2016) 0.80
Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease. Biol Direct (2015) 0.79
Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity. Genome Biol Evol (2016) 0.78
A bend, flip and trap mechanism for transposon integration. Elife (2016) 0.78
Virus-host arms race at the joint origin of multicellularity and programmed cell death. Cell Cycle (2014) 0.78
A decade of discovery: CRISPR functions and applications. Nat Microbiol (2017) 0.77
The Bacteriophage Carrier State of Campylobacter jejuni Features Changes in Host Non-coding RNAs and the Acquisition of New Host-derived CRISPR Spacer Sequences. Front Microbiol (2016) 0.77
Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems. Nucleic Acids Res (2016) 0.76
Five big mysteries about CRISPR's origins. Nature (2017) 0.75
Mobile genetic elements: in silico, in vitro, in vivo. Mol Ecol (2016) 0.75
Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct (2017) 0.75
Horizontal transfer - imperative mission of acellular life forms, Acytota. Mob Genet Elements (2016) 0.75
Mechanism of spacer integration links the CRISPR/Cas system to transposition as a form of mobile DNA. Mob DNA (2015) 0.75
CRISPR-cas Adaptive Immunity and the Three Rs. Biosci Rep (2017) 0.75
Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity. Curr Opin Virol (2017) 0.75
Recruitment of CRISPR-Cas systems by Tn7-like transposons. Proc Natl Acad Sci U S A (2017) 0.75
Transposable Element Domestication As an Adaptation to Evolutionary Conflicts. Trends Genet (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol (2013) 112.81
The sequence of the human genome. Science (2001) 101.55
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res (2005) 23.41
Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
CD-Search: protein domain annotations on the fly. Nucleic Acids Res (2004) 16.76
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol (2009) 15.15
Insertion sequences. Microbiol Mol Biol Rev (1998) 14.03
A unified classification system for eukaryotic transposable elements. Nat Rev Genet (2007) 11.03
Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature (2005) 9.83
ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res (2006) 9.58
Bacteriophage resistance mechanisms. Nat Rev Microbiol (2010) 7.38
PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 7.16
Prophages and bacterial genomics: what have we learned so far? Mol Microbiol (2003) 6.84
Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68
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
Mechanisms of site-specific recombination. Annu Rev Biochem (2006) 4.29
Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun (2012) 4.04
Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res (2012) 4.03
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics (2012) 3.83
Comparison of ARM and HEAT protein repeats. J Mol Biol (2001) 3.78
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol (2005) 3.50
Protein-priming of DNA replication. Annu Rev Biochem (1991) 3.49
Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure (2009) 3.47
A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet (2008) 3.17
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science (2002) 2.69
The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu Rev Genet (2012) 2.56
Integrons. Annu Rev Genet (2010) 2.54
Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol (2014) 2.21
Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet (2007) 2.17
Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res (2000) 2.01
Tn7: smarter than we thought. Nat Rev Mol Cell Biol (2001) 2.00
Comparative architecture of transposase and integrase complexes. Nat Struct Biol (2001) 1.99
Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol (2002) 1.91
Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res (2014) 1.91
The deep archaeal roots of eukaryotes. Mol Biol Evol (2008) 1.90
A modular master on the move: the Tn916 family of mobile genetic elements. Trends Microbiol (2009) 1.86
Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res (2013) 1.82
Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene (2006) 1.66
Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci U S A (2006) 1.65
The struggle for life of the genome's selfish architects. Biol Direct (2011) 1.64
CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol (2013) 1.45
A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature (2006) 1.44
Insertion sequence diversity in archaea. Microbiol Mol Biol Rev (2007) 1.41
CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA (2013) 1.33
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
His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology (2006) 1.33
A virocentric perspective on the evolution of life. Curr Opin Virol (2013) 1.29
Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol (2013) 1.28
Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species. J Bacteriol (2012) 1.28
The basic building blocks and evolution of CRISPR-CAS systems. Biochem Soc Trans (2013) 1.23
Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi. Microbiology (2003) 1.14
Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Appl Environ Microbiol (2010) 1.12
Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol Direct (2014) 1.10
A new group of tyrosine recombinase-encoding retrotransposons. Mol Biol Evol (2004) 1.08
A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. Genome Biol (2004) 1.05
The repetitive DNA content of eukaryotic genomes. Genome Dyn (2012) 1.04
Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid (2008) 1.02
Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol (2013) 0.99
Unification of the globally distributed spindle-shaped viruses of the Archaea. J Virol (2013) 0.99
The major role of viruses in cellular evolution: facts and hypotheses. Curr Opin Virol (2013) 0.98
Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol (2010) 0.97
Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J Virol (2012) 0.96
Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity. Biochem Biophys Res Commun (2013) 0.91
Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle. J Bacteriol (2012) 0.90
A superfamily of DNA transposons targeting multicopy small RNA genes. PLoS One (2013) 0.90
Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses. Sci Rep (2014) 0.88
Epigenetic regulation of Mammalian genomes by transposable elements. Ann N Y Acad Sci (2009) 0.86
A proposed mechanism for IS607-family serine transposases. Mob DNA (2013) 0.80
Analysis of retrotransposon activity in plants. Methods Mol Biol (2014) 0.77
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
Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol (2008) 5.31
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
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
The virophage as a unique parasite of the giant mimivirus. Nature (2008) 4.09
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
An alternative flavin-dependent mechanism for thymidylate synthesis. Science (2002) 3.82
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
Redefining viruses: lessons from Mimivirus. Nat Rev Microbiol (2008) 3.27
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
An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol (2003) 2.75
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
Viruses of the Archaea: a unifying view. Nat Rev Microbiol (2006) 2.61
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
ATGL has a key role in lipid droplet/adiposome degradation in mammalian cells. EMBO Rep (2006) 2.26
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
Evolutionary significance of gene expression divergence. Gene (2004) 2.04
Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol (2006) 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
Microevolutionary genomics of bacteria. Theor Popul Biol (2002) 1.95
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
Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol (2004) 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
Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res (2010) 1.93
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A (2005) 1.93
Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol (2002) 1.92
GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep (2006) 1.91