Published in Biol Direct on June 03, 2009
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS Genet (2009) 2.89
The phage-host arms race: shaping the evolution of microbes. Bioessays (2011) 2.27
Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc Natl Acad Sci U S A (2010) 2.20
Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res (2011) 2.19
Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res (2010) 1.93
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea. Nucleic Acids Res (2010) 1.83
Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res (2013) 1.82
Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes. EMBO J (2011) 1.76
CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol (2013) 1.58
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct (2009) 1.58
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science (2016) 1.56
Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol (2011) 1.53
To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res (2013) 1.42
Expression of the Streptococcus pneumoniae yoeB chromosomal toxin gene causes cell death in the model plant Arabidopsis thaliana. BMC Biotechnol (2015) 1.41
Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes. Nucleic Acids Res (2012) 1.40
Toxin-antitoxin systems as multilevel interaction systems. Toxins (Basel) (2014) 1.36
Virulence factors of the oral spirochete Treponema denticola. J Dent Res (2010) 1.35
Bacterial genome instability. Microbiol Mol Biol Rev (2014) 1.31
A virocentric perspective on the evolution of life. Curr Opin Virol (2013) 1.29
Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol Direct (2012) 1.27
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res (2011) 1.25
Multiple toxin-antitoxin systems in Mycobacterium tuberculosis. Toxins (Basel) (2014) 1.24
Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems. Mol Microbiol (2010) 1.24
A processed noncoding RNA regulates an altruistic bacterial antiviral system. Nat Struct Mol Biol (2011) 1.24
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct (2013) 1.14
The TetR family of regulators. Microbiol Mol Biol Rev (2013) 1.14
Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol (2012) 1.11
A toxin-antitoxin module of Salmonella promotes virulence in mice. PLoS Pathog (2013) 1.08
Structural basis of defects in the sacsin HEPN domain responsible for autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS). J Biol Chem (2011) 1.08
A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis. Nucleic Acids Res (2011) 1.07
Txe, an endoribonuclease of the enterococcal Axe-Txe toxin-antitoxin system, cleaves mRNA and inhibits protein synthesis. Microbiology (2010) 1.06
The Escherichia coli mqsR and ygiT genes encode a new toxin-antitoxin pair. J Bacteriol (2010) 1.06
Regulation of enteric vapBC transcription: induction by VapC toxin dimer-breaking. Nucleic Acids Res (2012) 1.06
Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning. Mol Cell (2013) 1.05
A stress-inducible quorum-sensing peptide mediates the formation of persister cells with noninherited multidrug tolerance. J Bacteriol (2012) 1.05
Massive activation of archaeal defense genes during viral infection. J Virol (2013) 1.03
Phage ϕC2 mediates transduction of Tn6215, encoding erythromycin resistance, between Clostridium difficile strains. MBio (2013) 1.02
Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS Negl Trop Dis (2012) 1.02
Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biol (2013) 1.02
Toxin-antitoxin (TA) systems are prevalent and transcribed in clinical isolates of Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus. FEMS Microbiol Lett (2011) 1.02
Analyzing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. J Bacteriol (2010) 1.01
Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids. PLoS One (2013) 1.01
Crystal structure of the VapBC toxin-antitoxin complex from Shigella flexneri reveals a hetero-octameric DNA-binding assembly. J Mol Biol (2011) 1.01
The relBE2Spn toxin-antitoxin system of Streptococcus pneumoniae: role in antibiotic tolerance and functional conservation in clinical isolates. PLoS One (2010) 1.00
Regulating toxin-antitoxin expression: controlled detonation of intracellular molecular timebombs. Toxins (Basel) (2014) 1.00
Identification of the first functional toxin-antitoxin system in Streptomyces. PLoS One (2012) 1.00
Doc toxin is a kinase that inactivates elongation factor Tu. J Biol Chem (2014) 0.99
A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res (2014) 0.97
Transcriptional cross-activation between toxin-antitoxin systems of Escherichia coli. BMC Microbiol (2013) 0.96
The chromosomal mazEF locus of Streptococcus mutans encodes a functional type II toxin-antitoxin addiction system. J Bacteriol (2010) 0.96
VapC6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote Sulfolobus solfataricus. RNA (2011) 0.96
Toxin-antitoxin genes of the Gram-positive pathogen Streptococcus pneumoniae: so few and yet so many. Microbiol Mol Biol Rev (2012) 0.94
The Yersinia pestis chromosome encodes active addiction toxins. J Bacteriol (2010) 0.93
Identification and characterization of type II toxin-antitoxin systems in the opportunistic pathogen Acinetobacter baumannii. J Bacteriol (2013) 0.92
Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles (2014) 0.92
A toxin-antitoxin module in Bacillus subtilis can both mitigate and amplify effects of lethal stress. PLoS One (2011) 0.91
Myxococcus xanthus developmental cell fate production: heterogeneous accumulation of developmental regulatory proteins and reexamination of the role of MazF in developmental lysis. J Bacteriol (2012) 0.91
Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling. Genome Biol Evol (2013) 0.91
Characterization of a Streptococcus mutans intergenic region containing a small toxic peptide and its cis-encoded antisense small RNA antitoxin. PLoS One (2013) 0.90
Spontaneously induced prophages in Lactobacillus gasseri contribute to horizontal gene transfer. Appl Environ Microbiol (2014) 0.89
Genetic regulation of the yefM-yoeB toxin-antitoxin locus of Streptococcus pneumoniae. J Bacteriol (2011) 0.89
Characterization of a chromosomal type II toxin-antitoxin system mazEaFa in the Cyanobacterium Anabaena sp. PCC 7120. PLoS One (2013) 0.88
sRNA antitoxins: more than one way to repress a toxin. Toxins (Basel) (2014) 0.88
The proteolytic activation of the relNEs (ssr1114/slr0664) toxin-antitoxin system by both proteases Lons and ClpP2s/Xs of Synechocystis sp. PCC 6803. Curr Microbiol (2011) 0.88
Persisters-as elusive as ever. Appl Microbiol Biotechnol (2016) 0.87
Isolation of highly persistent mutants of Salmonella enterica serovar typhimurium reveals a new toxin-antitoxin module. J Bacteriol (2012) 0.86
Analysis of SOS-induced spontaneous prophage induction in Corynebacterium glutamicum at the single-cell level. J Bacteriol (2013) 0.86
Toxin-Antitoxin Systems in Clinical Pathogens. Toxins (Basel) (2016) 0.86
Recent advancements in toxin and antitoxin systems involved in bacterial programmed cell death. Int J Microbiol (2010) 0.85
Molecular structure and function of the novel BrnT/BrnA toxin-antitoxin system of Brucella abortus. J Biol Chem (2012) 0.85
TAC from Mycobacterium tuberculosis: a paradigm for stress-responsive toxin-antitoxin systems controlled by SecB-like chaperones. Cell Stress Chaperones (2012) 0.85
Chromosomal islands of Streptococcus pyogenes and related streptococci: molecular switches for survival and virulence. Front Cell Infect Microbiol (2014) 0.84
Post-transcriptional regulation of gene expression in bacterial pathogens by toxin-antitoxin systems. Front Cell Infect Microbiol (2014) 0.83
A bird's-eye view of autophagy. Autophagy (2013) 0.83
Toxin-antitoxin systems on the large defense plasmid pSYSA of Synechocystis sp. PCC 6803. J Biol Chem (2013) 0.83
Functional validation of putative toxin-antitoxin genes from the Gram-positive pathogen Streptococcus pneumoniae: phd-doc is the fourth bona-fide operon. Front Microbiol (2014) 0.83
The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8. BMC Genomics (2014) 0.82
Type II toxin: antitoxin systems. More than small selfish entities? Curr Genet (2015) 0.82
Protein expression, crystallization and preliminary X-ray crystallographic analysis of the isolated Shigella flexneri VapC toxin. Acta Crystallogr Sect F Struct Biol Cryst Commun (2013) 0.82
A moderate toxin, GraT, modulates growth rate and stress tolerance of Pseudomonas putida. J Bacteriol (2013) 0.81
Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes. Structure (2013) 0.81
Characterization of MazF-Mediated Sequence-Specific RNA Cleavage in Pseudomonas putida Using Massive Parallel Sequencing. PLoS One (2016) 0.80
Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin. BMC Genomics (2014) 0.80
Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems. BMC Evol Biol (2015) 0.80
Classification of prokaryotic genetic replicators: between selfishness and altruism. Ann N Y Acad Sci (2015) 0.80
Viruses and mobile elements as drivers of evolutionary transitions. Philos Trans R Soc Lond B Biol Sci (2016) 0.80
Cell growth inhibition upon deletion of four toxin-antitoxin loci from the megaplasmids of Sinorhizobium meliloti. J Bacteriol (2013) 0.80
Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. Genome Biol Evol (2013) 0.79
Multitasking SecB chaperones in bacteria. Front Microbiol (2014) 0.79
Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question. Stud Hist Philos Biol Biomed Sci (2016) 0.79
AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea. Toxins (Basel) (2016) 0.79
The ecology of bacterial genes and the survival of the new. Int J Evol Biol (2012) 0.78
Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae. Biol Direct (2015) 0.78
Structure-function analysis of VapB4 antitoxin identifies critical features of a minimal VapC4 toxin-binding module. J Bacteriol (2015) 0.78
Plasmids of carotenoid-producing Paracoccus spp. (Alphaproteobacteria) - structure, diversity and evolution. PLoS One (2013) 0.78
Virus-host arms race at the joint origin of multicellularity and programmed cell death. Cell Cycle (2014) 0.78
Crystallization of the HigBA2 toxin-antitoxin complex from Vibrio cholerae. Acta Crystallogr Sect F Struct Biol Cryst Commun (2013) 0.78
Orphan toxin OrtT (YdcX) of Escherichia coli reduces growth during the stringent response. Toxins (Basel) (2015) 0.78
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
The PSIPRED protein structure prediction server. Bioinformatics (2000) 20.58
CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res (2002) 18.54
Prokaryotic toxin-antitoxin stress response loci. Nat Rev Microbiol (2005) 9.08
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
Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res (2005) 6.61
Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol (2005) 5.77
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res (2000) 5.68
An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death. Proc Natl Acad Sci U S A (1996) 5.25
Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol Microbiol (2000) 5.08
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78
Complete nucleotide sequence and gene organization of the broad-host-range plasmid RSF1010. Gene (1989) 4.70
MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell (2003) 4.63
Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science (2003) 4.55
Structure and functions of the GNAT superfamily of acetyltransferases. Arch Biochem Biophys (2005) 4.36
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res (2001) 4.22
The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol (2007) 4.14
Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proc Natl Acad Sci U S A (1983) 4.07
Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol (2000) 4.04
Activation of the ATPase activity of hsp90 by the stress-regulated cochaperone aha1. Mol Cell (2002) 3.89
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res (1999) 3.62
Programmed death in bacteria. Microbiol Mol Biol Rev (2000) 3.49
Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol Microbiol (2002) 3.44
DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res (1999) 3.32
The MerR family of transcriptional regulators. FEMS Microbiol Rev (2003) 3.30
Scaling laws in the functional content of genomes. Trends Genet (2003) 3.23
Multidrug tolerance of biofilms and persister cells. Curr Top Microbiol Immunol (2008) 3.19
Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). J Bacteriol (2006) 3.14
One-component systems dominate signal transduction in prokaryotes. Trends Microbiol (2005) 3.09
Properties of the defective phage of Bacillus subtilis. J Mol Biol (1968) 3.09
Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet (2009) 3.03
Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci U S A (2002) 2.95
Toxin-antitoxin modules as bacterial metabolic stress managers. Trends Biochem Sci (2005) 2.88
Hypothetical functions of toxin-antitoxin systems. J Bacteriol (2007) 2.81
Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol (2005) 2.78
New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol (2003) 2.77
Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science (2009) 2.74
MazF, an mRNA interferase, mediates programmed cell death during multicellular Myxococcus development. Cell (2008) 2.70
The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc Natl Acad Sci U S A (2009) 2.69
Escherichia coli mazEF-mediated cell death is triggered by various stressful conditions. J Bacteriol (2004) 2.66
Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins (2001) 2.65
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci U S A (2001) 2.59
Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J (1986) 2.54
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance. FEMS Microbiol Rev (2003) 2.51
Small toxic proteins and the antisense RNAs that repress them. Microbiol Mol Biol Rev (2008) 2.42
What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome? J Bacteriol (2007) 2.29
HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea. J Bacteriol (2008) 2.26
PIN domains in nonsense-mediated mRNA decay and RNAi. Curr Biol (2001) 2.26
RNA antitoxins. Curr Opin Microbiol (2007) 2.26
An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol (2007) 2.11
Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol (2006) 2.04
RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes. Genome Biol (2007) 1.96
The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding. Proc Natl Acad Sci U S A (1991) 1.93
A conserved anti-repressor controls horizontal gene transfer by proteolysis. Mol Microbiol (2008) 1.92
A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology (2004) 1.84
The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol (2005) 1.84
Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics (2004) 1.80
Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol (2008) 1.79
mRNA interferases, sequence-specific endoribonucleases from the toxin-antitoxin systems. Prog Mol Biol Transl Sci (2009) 1.77
Toxin-antitoxin systems are ubiquitous and plasmid-encoded in vancomycin-resistant enterococci. Proc Natl Acad Sci U S A (2006) 1.68
Guilt by association: contextual information in genome analysis. Genome Res (2000) 1.65
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics (2006) 1.60
Aha1 binds to the middle domain of Hsp90, contributes to client protein activation, and stimulates the ATPase activity of the molecular chaperone. J Biol Chem (2003) 1.57
Potential genomic determinants of hyperthermophily. Trends Genet (2003) 1.54
Prediction of protein function and pathways in the genome era. Cell Mol Life Sci (2004) 1.49
Chromosomal toxin-antitoxin systems may act as antiaddiction modules. J Bacteriol (2008) 1.46
The communication factor EDF and the toxin-antitoxin module mazEF determine the mode of action of antibiotics. PLoS Biol (2008) 1.45
Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Nucleic Acids Res (2005) 1.44
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Genome Biol (2002) 1.34
PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans. Biochem Biophys Res Commun (2003) 1.30
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res (2008) 1.30
The bldB gene encodes a small protein required for morphogenesis, antibiotic production, and catabolite control in Streptomyces coelicolor. J Bacteriol (1998) 1.26
Delayed-relaxed response explained by hyperactivation of RelE. Mol Microbiol (2004) 1.25
The tripartite immunity system of phages P1 and P7. FEMS Microbiol Rev (1995) 1.25
Bacterial persistence: some new insights into an old phenomenon. J Biosci (2008) 1.25
The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression. J Bacteriol (2002) 1.22
Structural features of a superfamily of zinc-endopeptidases: the metzincins. Curr Opin Struct Biol (1995) 1.22
The major birch pollen allergen, Bet v 1, shows ribonuclease activity. Planta (1996) 1.17
BzdR, a repressor that controls the anaerobic catabolism of benzoate in Azoarcus sp. CIB, is the first member of a new subfamily of transcriptional regulators. J Biol Chem (2005) 1.17
Analysis of sequences flanking the vap regions of Dichelobacter nodosus: evidence for multiple integration events, a killer system, and a new genetic element. Microbiology (1997) 1.16
Regulation of NAD synthesis by the trifunctional NadR protein of Salmonella enterica. J Bacteriol (2005) 1.16
Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA). ISME J (2008) 1.14
Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR. J Struct Biol (2005) 1.14
Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. FEBS Lett (2005) 1.12
Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for beta-lactam acetylation. J Mol Biol (2003) 1.12
The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2. J Bacteriol (2006) 1.11
Crystal structure of MtaN, a global multidrug transporter gene activator. J Biol Chem (2001) 1.11
Automated discovery and phylogenetic analysis of new toxin-antitoxin systems. BMC Microbiol (2008) 1.08
Structure and regulation of the lytic replicon of phage P1. J Mol Biol (1989) 1.08
Resistance to enediyne antitumor antibiotics by CalC self-sacrifice. Science (2003) 1.08
HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins. Trends Biochem Sci (2003) 1.03
Defining the mobilome. Methods Mol Biol (2009) 1.03
RNA decay by messenger RNA interferases. Methods Enzymol (2008) 1.02
Genetic control of bacterial suicide: regulation of the induction of PBSX in Bacillus subtilis. J Bacteriol (1994) 1.00
Cloning and nucleotide sequence of the Bacillus subtilis ansR gene, which encodes a repressor of the ans operon coding for L-asparaginase and L-aspartase. J Bacteriol (1993) 1.00
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. BMC Genomics (2005) 0.97
Structural insight into the self-sacrifice mechanism of enediyne resistance. ACS Chem Biol (2006) 0.96
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
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
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
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
The structure of the protein universe and genome evolution. Nature (2002) 4.47
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
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
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol (2008) 2.74
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
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
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
The relationship of protein conservation and sequence length. BMC Evol Biol (2002) 1.95