Published in J Bacteriol on October 13, 2006
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct (2009) 3.17
Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol (2010) 3.12
Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet (2009) 3.03
Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science (2009) 2.74
Molecular control of bacterial death and lysis. Microbiol Mol Biol Rev (2008) 2.52
Genome sequence of hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and comparative genomics with V. cholerae. J Bacteriol (2010) 2.50
SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet (2009) 2.28
Four-jointed is a Golgi kinase that phosphorylates a subset of cadherin domains. Science (2008) 2.28
Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. J Bacteriol (2010) 2.11
Comparative genomics of the IncA/C multidrug resistance plasmid family. J Bacteriol (2009) 2.06
Legionella pneumophila pangenome reveals strain-specific virulence factors. BMC Genomics (2010) 1.98
PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli. Antimicrob Agents Chemother (2007) 1.85
Secreted protein kinases. Trends Biochem Sci (2012) 1.79
A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat Chem Biol (2012) 1.67
Characterization and transcriptome analysis of Mycobacterium tuberculosis persisters. MBio (2011) 1.64
Four-jointed modulates growth and planar polarity by reducing the affinity of dachsous for fat. Curr Biol (2010) 1.54
HipBA-promoter structures reveal the basis of heritable multidrug tolerance. Nature (2015) 1.53
Heterogeneous bacterial persisters and engineering approaches to eliminate them. Curr Opin Microbiol (2011) 1.47
Patients with long-term oral carriage harbor high-persister mutants of Candida albicans. Antimicrob Agents Chemother (2009) 1.46
Bacterial toxin HigB associates with ribosomes and mediates translation-dependent mRNA cleavage at A-rich sites. J Biol Chem (2009) 1.44
To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res (2013) 1.42
Role of oxidative stress in persister tolerance. Antimicrob Agents Chemother (2012) 1.40
Stochastic mechanisms of cell fate specification that yield random or robust outcomes. Annu Rev Cell Dev Biol (2010) 1.32
A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS. J Proteome Res (2007) 1.29
Staphylococcus aureus persisters tolerant to bactericidal antibiotics. J Mol Microbiol Biotechnol (2012) 1.25
Pharmacodynamics, population dynamics, and the evolution of persistence in Staphylococcus aureus. PLoS Genet (2013) 1.23
Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases. Proc Natl Acad Sci U S A (2015) 1.10
The intrinsic resistome of bacterial pathogens. Front Microbiol (2013) 1.05
HipA-triggered growth arrest and β-lactam tolerance in Escherichia coli are mediated by RelA-dependent ppGpp synthesis. J Bacteriol (2013) 1.03
Crystal structure of the DNA-bound VapBC2 antitoxin/toxin pair from Rickettsia felis. Nucleic Acids Res (2011) 0.98
Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC Microbiol (2013) 0.98
Transcriptional cross-activation between toxin-antitoxin systems of Escherichia coli. BMC Microbiol (2013) 0.96
Regulation of the Escherichia coli HipBA toxin-antitoxin system by proteolysis. PLoS One (2012) 0.96
Role of vapBC toxin-antitoxin loci in the thermal stress response of Sulfolobus solfataricus. Biochem Soc Trans (2009) 0.95
The Escherichia coli toxin MqsR destabilizes the transcriptional repression complex formed between the antitoxin MqsA and the mqsRA operon promoter. J Biol Chem (2012) 0.89
Heterogeneous persister cells formation in Acinetobacter baumannii. PLoS One (2013) 0.88
Enhancing the utility of existing antibiotics by targeting bacterial behaviour? Br J Pharmacol (2012) 0.88
Role of unusual P loop ejection and autophosphorylation in HipA-mediated persistence and multidrug tolerance. Cell Rep (2012) 0.87
Global expression profile of biofilm resistance to antimicrobial compounds in the plant-pathogenic bacterium Xylella fastidiosa reveals evidence of persister cells. J Bacteriol (2012) 0.87
Peptide-lipid interactions of the stress-response peptide TisB that induces bacterial persistence. Biophys J (2012) 0.86
Isolation of highly persistent mutants of Salmonella enterica serovar typhimurium reveals a new toxin-antitoxin module. J Bacteriol (2012) 0.86
Hsp33 controls elongation factor-Tu stability and allows Escherichia coli growth in the absence of the major DnaK and trigger factor chaperones. J Biol Chem (2012) 0.86
VapC from the leptospiral VapBC toxin-antitoxin module displays ribonuclease activity on the initiator tRNA. PLoS One (2014) 0.86
Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility. Front Microbiol (2013) 0.85
Recent advancements in toxin and antitoxin systems involved in bacterial programmed cell death. Int J Microbiol (2010) 0.85
Growth feedback as a basis for persister bistability. Proc Natl Acad Sci U S A (2013) 0.83
Functional and structural analysis of HicA3-HicB3, a novel toxin-antitoxin system of Yersinia pestis. J Bacteriol (2014) 0.82
Type II toxin: antitoxin systems. More than small selfish entities? Curr Genet (2015) 0.82
The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence. Nucleic Acids Res (2014) 0.81
Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF. J Biol Chem (2016) 0.81
High Persister Mutants in Mycobacterium tuberculosis. PLoS One (2016) 0.78
Persister formation in Staphylococcus aureus is associated with ATP depletion. Nat Microbiol (2016) 0.78
Identification and characterization of chromosomal relBE toxin-antitoxin locus in Streptomyces cattleya DSM46488. Sci Rep (2016) 0.76
Identification and characterization of a HEPN-MNT family type II toxin-antitoxin in Shewanella oneidensis. Microb Biotechnol (2015) 0.76
Wake me when it's over - Bacterial toxin-antitoxin proteins and induced dormancy. Exp Biol Med (Maywood) (2016) 0.76
A Proteomic Signature of Dormancy in an Actinobacterium: Micrococcus luteus. J Bacteriol (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol (1995) 46.37
Bacterial persistence as a phenotypic switch. Science (2004) 15.80
Prokaryotic toxin-antitoxin stress response loci. Nat Rev Microbiol (2005) 9.08
Riddle of biofilm resistance. Antimicrob Agents Chemother (2001) 7.19
Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res (2005) 6.61
Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol (2004) 5.82
Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett (2004) 5.23
hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol (1983) 4.59
Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials. J Bacteriol (2001) 4.49
Persisters: a distinct physiological state of E. coli. BMC Microbiol (2006) 4.03
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
Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal Chem (1997) 3.09
Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol Microbiol (2003) 2.92
A dose-response study of antibiotic resistance in Pseudomonas aeruginosa biofilms. Antimicrob Agents Chemother (2000) 2.91
Molecular cloning and expression of hipA, a gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol (1986) 2.50
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol (2000) 2.45
Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol (1991) 2.37
Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol (1994) 2.33
Phenotypic tolerance: antibiotic enrichment of noninherited resistance in bacterial populations. Antimicrob Agents Chemother (2005) 2.20
Increased persistence in Escherichia coli caused by controlled expression of toxins or other unrelated proteins. J Bacteriol (2006) 2.19
Ectopic overexpression of wild-type and mutant hipA genes in Escherichia coli: effects on macromolecular synthesis and persister formation. J Bacteriol (2006) 2.17
Joint tolerance to beta-lactam and fluoroquinolone antibiotics in Escherichia coli results from overexpression of hipA. Antimicrob Agents Chemother (1998) 1.92
Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci U S A (2005) 1.83
A novel family of Escherichia coli toxin-antitoxin gene pairs. J Bacteriol (2003) 1.68
GlpD and PlsB participate in persister cell formation in Escherichia coli. J Bacteriol (2006) 1.66
Crystal structure of the plasmid maintenance system epsilon/zeta: functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation. Proc Natl Acad Sci U S A (2003) 1.64
A novel family of phosphatidylinositol 4-kinases conserved from yeast to humans. J Biol Chem (2001) 1.62
Persister cells, the biofilm matrix and tolerance to metal cations in biofilm and planktonic Pseudomonas aeruginosa. Environ Microbiol (2005) 1.36
Persister cells mediate tolerance to metal oxyanions in Escherichia coli. Microbiology (2005) 1.12
Analysis of the catalytic domain of phosphatidylinositol 4-kinase type II. J Biol Chem (2002) 1.06
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
Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol (2004) 5.82
Selection in the evolution of gene duplications. Genome Biol (2002) 5.58
Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett (2004) 5.23
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 Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol (2005) 4.28
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
Persisters: a distinct physiological state of E. coli. BMC Microbiol (2006) 4.03
Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00
Tackling antibiotic resistance. Nat Rev Microbiol (2011) 3.95
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
Introns and the origin of nucleus-cytosol compartmentalization. Nature (2006) 3.16
Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol (2010) 3.12
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
Killing by bactericidal antibiotics does not depend on reactive oxygen species. Science (2013) 2.97
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
Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science (2009) 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
Role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli. Antimicrob Agents Chemother (2008) 2.40
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet (2004) 2.40
Explosive spread and high prevalence of HIV infection among injecting drug users in Togliatti City, Russia. AIDS (2002) 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
SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet (2009) 2.28
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
Candida albicans biofilms produce antifungal-tolerant persister cells. Antimicrob Agents Chemother (2006) 2.18
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
Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. J Bacteriol (2010) 2.11
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
Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem Biol (2010) 2.04
Evolutionary significance of gene expression divergence. Gene (2004) 2.04
Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol (2007) 2.03
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
High-throughput screen for novel antimicrobials using a whole animal infection model. ACS Chem Biol (2009) 1.99
Identification of novel antimicrobials using a live-animal infection model. Proc Natl Acad Sci U S A (2006) 1.98
Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A (2012) 1.96
Multidrug pump inhibitors uncover remarkable activity of plant antimicrobials. Antimicrob Agents Chemother (2002) 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
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
CNS expression of glucocerebrosidase corrects alpha-synuclein pathology and memory in a mouse model of Gaucher-related synucleinopathy. Proc Natl Acad Sci U S A (2011) 1.90
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
Evaluation of a modified commercial assay in detecting antibody to hepatitis C virus in oral fluids and dried blood spots. J Med Virol (2003) 1.84
Phylogenomics of prokaryotic ribosomal proteins. PLoS One (2012) 1.82