Whole-genome mutational biases in bacteria.

Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol (2011) 4.67

Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet (2010) 2.95

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci U S A (2012) 2.47

Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet (2009) 2.11

Genome dynamics during experimental evolution. Nat Rev Genet (2013) 2.07

Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome. J Bacteriol (2009) 1.83

Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol (2011) 1.78

The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nat Rev Genet (2010) 1.58

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. G3 (Bethesda) (2011) 1.53

Whole-genome sequencing of a laboratory-evolved yeast strain. BMC Genomics (2010) 1.34

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria? PLoS Genet (2010) 1.30

New insights into bacterial adaptation through in vivo and in silico experimental evolution. Nat Rev Microbiol (2012) 1.28

No gene-specific optimization of mutation rate in Escherichia coli. Mol Biol Evol (2013) 1.13

On the molecular mechanism of GC content variation among eubacterial genomes. Biol Direct (2012) 1.13

Determinants of the rate of protein sequence evolution. Nat Rev Genet (2015) 1.09

An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia. Genome Biol Evol (2011) 1.09

Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev (2014) 1.04

Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol (2011) 1.04

The Presence of the DNA Repair Genes mutM, mutY, mutL, and mutS is Related to Proteome Size in Bacterial Genomes. Front Genet (2012) 1.00

Yeast mutation accumulation experiment supports elevated mutation rates at highly transcribed sites. Proc Natl Acad Sci U S A (2014) 1.00

Phenotypic diversity caused by differential RpoS activity among environmental Escherichia coli isolates. Appl Environ Microbiol (2011) 0.99

Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS One (2013) 0.98

Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. ISME J (2014) 0.96

Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus. Genome Biol Evol (2010) 0.94

Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences. Future Microbiol (2012) 0.93

Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res (2013) 0.91

Genome-wide characterization of Vibrio phage φpp2 with unique arrangements of the mob-like genes. BMC Genomics (2012) 0.90

Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans. Mol Biol Evol (2015) 0.87

The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia. Genetics (2015) 0.87

Mutation frequency and spectrum of mutations vary at different chromosomal positions of Pseudomonas putida. PLoS One (2012) 0.86

Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes. PLoS One (2013) 0.86

Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons. J Bacteriol (2014) 0.85

Temperature adaptation at homologous sites in proteins from nine thermophile-mesophile species pairs. Genome Biol Evol (2010) 0.85

Loss of genes for DNA recombination and repair in the reductive genome evolution of thioautotrophic symbionts of Calyptogena clams. BMC Evol Biol (2011) 0.85

Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini. PeerJ (2015) 0.84

Experimental evolution in biofilm populations. FEMS Microbiol Rev (2016) 0.84

Phylogenomic analysis of the uracil-DNA glycosylase superfamily. Mol Biol Evol (2010) 0.84

Genome cartography: charting the apicomplexan genome. Trends Parasitol (2011) 0.83

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea. BMC Genomics (2015) 0.83

Quantifying position-dependent codon usage bias. Mol Biol Evol (2014) 0.82

Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles. Proc Natl Acad Sci U S A (2016) 0.82

Escherichia coli frameshift mutation rate depends on the chromosomal context but not on the GATC content near the mutation site. PLoS One (2012) 0.81

A blueprint for a mutationist theory of replicative strand asymmetries formation. Curr Genomics (2012) 0.81

Evolution of genome base composition and genome size in bacteria. Front Microbiol (2012) 0.81

The Effect of Local Sequence Context on Mutational Bias of Genes Encoded on the Leading and Lagging Strands. Curr Biol (2016) 0.80

A phyletically rare gene promotes the niche-specific fitness of an E. coli pathogen during bacteremia. PLoS Pathog (2013) 0.80

The properties of spontaneous mutations in the opportunistic pathogen Pseudomonas aeruginosa. BMC Genomics (2016) 0.78

tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria. PLoS Comput Biol (2014) 0.77

Nascent RNA folding mitigates transcription-associated mutagenesis. Genome Res (2015) 0.77

Replication-Associated Mutational Pressure (RMP) Governs Strand-Biased Compositional Asymmetry (SCA) and Gene Organization in Animal Mitochondrial Genomes. Curr Genomics (2012) 0.77

The Genome of Haemoproteus tartakovskyi and Its Relationship to Human Malaria Parasites. Genome Biol Evol (2016) 0.76

Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra. PLoS Genet (2017) 0.76

Reduced genome size of Helicobacter pylori originating from East Asia. World J Gastroenterol (2014) 0.76

Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics. Nucleic Acids Res (2014) 0.75

Spontaneous mutation rate in the smallest photosynthetic eukaryotes. Mol Biol Evol (2017) 0.75

Effects of Genic Base Composition on Growth Rate in G+C-rich Genomes. G3 (Bethesda) (2015) 0.75

Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Res (2017) 0.75

Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations. J Transl Med (2011) 0.75

Genome sequences characterizing five mutations in RNA polymerase and major capsid of phages ϕA318 and ϕAs51 of Vibrio alginolyticus with different burst efficiencies. BMC Genomics (2014) 0.75

Dynamic Acquisition and Loss of Dual-Obligate Symbionts in the Plant-Sap-Feeding Adelgidae (Hemiptera: Sternorrhyncha: Aphidoidea). Front Microbiol (2017) 0.75

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A (2000) 96.90

Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89

Molecular basis of base substitution hotspots in Escherichia coli. Nature (1978) 13.79

A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci U S A (1991) 11.66

Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A (1996) 7.54

Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol (1996) 7.18

Mutagenic deamination of cytosine residues in DNA. Nature (1980) 6.26

The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J Bacteriol (1992) 5.16

Estimate of the genomic mutation rate deleterious to overall fitness in E. coli. Nature (1996) 4.88

Reductive evolution of resident genomes. Trends Microbiol (1998) 4.38

The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol (1987) 4.30

Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNA. Proc Natl Acad Sci U S A (1992) 4.29

Determining mutation rates in bacterial populations. Methods (2000) 4.15

A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry (1990) 3.51

Base composition bias might result from competition for metabolic resources. Trends Genet (2002) 3.17

Prokaryotic DNA replication. Annu Rev Biochem (1992) 2.95

Escherichia coli K-12 mutants deficient in uracil-DNA glycosylase. J Bacteriol (1978) 2.85

Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene (1999) 2.40

Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes. J Mol Evol (2002) 1.85

Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat Genet (2005) 1.79

Asymmetries generated by transcription-coupled repair in enterobacterial genes. Science (1996) 1.77

Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair. Genetics (1991) 1.73

Chromosomal location and evolutionary rate variation in enterobacterial genes. Science (1989) 1.67

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics (2004) 1.62

Genomic GC level, optimal growth temperature, and genome size in prokaryotes. Biochem Biophys Res Commun (2006) 1.61

Inequality in mutation rates of the two strands of DNA. Nature (1987) 1.47

Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus. Hereditas (1998) 1.44

Sunlight ultraviolet and bacterial DNA base ratios. Science (1970) 1.39

HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res (2007) 1.30

Transcription-dependent increase in multiple classes of base substitution mutations in Escherichia coli. J Bacteriol (2002) 1.24

Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure. J Mol Evol (1995) 1.10

The role of the Escherichia coli mug protein in the removal of uracil and 3,N(4)-ethenocytosine from DNA. J Biol Chem (1999) 1.10

Transcription increases multiple spontaneous point mutations in Salmonella enterica. Nucleic Acids Res (2003) 1.08

Role of uracil-DNA glycosylase in the repair of deaminated cytosine residues of DNA in Escherichia coli. J Biochem (1978) 0.99

Escherichia coli DNA glycosylase Mug: a growth-regulated enzyme required for mutation avoidance in stationary-phase cells. Mol Microbiol (2001) 0.89

Correlation between thermal stability maps and genetic maps of double-stranded DNAs. Nucleic Acids Symp Ser (1982) 0.80

Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog (2011) 3.89

Ohno's dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A (2007) 3.10

Long-term persistence of resistant Enterococcus species after antibiotics to eradicate Helicobacter pylori. Ann Intern Med (2003) 3.04

Effect of rpoB mutations conferring rifampin resistance on fitness of Mycobacterium tuberculosis. Antimicrob Agents Chemother (2004) 2.53

Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium. Mol Microbiol (2002) 2.32

Predicting antibiotic resistance. Nat Rev Microbiol (2007) 2.28

Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. Res Microbiol (2004) 2.23

Real-time evolution of new genes by innovation, amplification, and divergence. Science (2012) 2.22

Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proc Natl Acad Sci U S A (2002) 2.15

Compensatory gene amplification restores fitness after inter-species gene replacements. Mol Microbiol (2010) 1.97

Biological costs and mechanisms of fosfomycin resistance in Escherichia coli. Antimicrob Agents Chemother (2003) 1.89

Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation. Genetics (2003) 1.80

Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat Genet (2005) 1.79

Origin of mutations under selection: the adaptive mutation controversy. Annu Rev Microbiol (2006) 1.76

Reduction of the fitness burden of quinolone resistance in Pseudomonas aeruginosa. J Antimicrob Chemother (2004) 1.75

Bacterial gene amplification: implications for the evolution of antibiotic resistance. Nat Rev Microbiol (2009) 1.73

Multiple pathways of selected gene amplification during adaptive mutation. Proc Natl Acad Sci U S A (2006) 1.62

Reducing the fitness cost of antibiotic resistance by amplification of initiator tRNA genes. Proc Natl Acad Sci U S A (2006) 1.56

Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac. Proc Natl Acad Sci U S A (2003) 1.49

Mutational robustness of ribosomal protein genes. Science (2010) 1.41

Comparative proteome analysis of Mycobacterium tuberculosis grown under aerobic and anaerobic conditions. Microbiology (2004) 1.39

Adaptive mutation: how growth under selection stimulates Lac(+) reversion by increasing target copy number. J Bacteriol (2004) 1.37

Establishment of a superficial skin infection model in mice by using Staphylococcus aureus and Streptococcus pyogenes. Antimicrob Agents Chemother (2005) 1.32

Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium. Genetics (2009) 1.25

Selection-driven gene loss in bacteria. PLoS Genet (2012) 1.22

Evidence that selected amplification of a bacterial lac frameshift allele stimulates Lac(+) reversion (adaptive mutation) with or without general hypermutability. Genetics (2002) 1.20

Selection of resistance at lethal and non-lethal antibiotic concentrations. Curr Opin Microbiol (2012) 1.18

Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak. J Antimicrob Chemother (2011) 1.17

Genetic analysis of colistin resistance in Salmonella enterica serovar Typhimurium. Antimicrob Agents Chemother (2009) 1.17

Mechanism and fitness costs of PR-39 resistance in Salmonella enterica serovar Typhimurium LT2. Antimicrob Agents Chemother (2008) 1.16

Experimental adaptation of Salmonella typhimurium to mice. Genetics (2004) 1.13

Fusidic acid-resistant mutants of Salmonella enterica serovar Typhimurium with low fitness in vivo are defective in RpoS induction. Antimicrob Agents Chemother (2003) 1.13

Nitrofurantoin resistance mechanism and fitness cost in Escherichia coli. J Antimicrob Chemother (2008) 1.13

The fitness cost of streptomycin resistance depends on rpsL mutation, carbon source and RpoS (sigmaS). Genetics (2009) 1.13

Compensatory evolution reveals functional interactions between ribosomal proteins S12, L14 and L19. J Mol Biol (2006) 1.11

Persistence of resistant Staphylococcus epidermidis after single course of clarithromycin. Emerg Infect Dis (2005) 1.10

The effect of genomic position on reversion of a lac frameshift mutation (lacIZ33) during non-lethal selection (adaptive mutation). Mol Microbiol (2002) 1.10

The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types. Genetics (2010) 1.08

Multiple mechanisms to ameliorate the fitness burden of mupirocin resistance in Salmonella typhimurium. Mol Microbiol (2007) 1.08

Dynamics of antibiotic resistant Mycobacterium tuberculosis during long-term infection and antibiotic treatment. PLoS One (2011) 1.06

Fitness of antibiotic resistant Staphylococcus epidermidis assessed by competition on the skin of human volunteers. J Antimicrob Chemother (2003) 1.06

Amplification-mutagenesis--how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation. Res Microbiol (2004) 1.05

The first major extended-spectrum beta-lactamase outbreak in Scandinavia was caused by clonal spread of a multiresistant Klebsiella pneumoniae producing CTX-M-15. APMIS (2008) 1.03

Evolution of new gene functions: simulation and analysis of the amplification model. Genetica (2008) 1.02

Bacteria with increased mutation frequency and antibiotic resistance are enriched in the commensal flora of patients with high antibiotic usage. J Antimicrob Chemother (2003) 0.99

Slow genetic divergence of Helicobacter pylori strains during long-term colonization. Infect Immun (2005) 0.98

Polymorphic mutation frequencies in Escherichia coli: emergence of weak mutators in clinical isolates. J Bacteriol (2004) 0.98

Restored fitness leads to long-term persistence of resistant Bacteroides strains in the human intestine. Anaerobe (2008) 0.98

The cyclotide cycloviolacin O2 from Viola odorata has potent bactericidal activity against Gram-negative bacteria. J Antimicrob Chemother (2010) 0.97

Mechanisms and fitness costs of resistance to antimicrobial peptides LL-37, CNY100HL and wheat germ histones. PLoS One (2013) 0.96

Beyond serial passages: new methods for predicting the emergence of resistance to novel antibiotics. Curr Opin Pharmacol (2011) 0.93

Mechanisms and physiological effects of protamine resistance in Salmonella enterica serovar Typhimurium LT2. J Antimicrob Chemother (2010) 0.93

Escape from growth restriction in small colony variants of Salmonella typhimurium by gene amplification and mutation. Mol Microbiol (2010) 0.93

The amplification model for adaptive mutation: simulations and analysis. Genetics (2004) 0.91

Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits. EMBO J (2010) 0.91

Pharmacodynamic model to describe the concentration-dependent selection of cefotaxime-resistant Escherichia coli. Antimicrob Agents Chemother (2005) 0.90

Genome-wide detection of spontaneous chromosomal rearrangements in bacteria. PLoS One (2012) 0.90

Rebuttal: adaptive point mutation (Rosenberg and Hastings). J Bacteriol (2004) 0.90

Caenorhabditis elegans as a model to determine fitness of antibiotic-resistant Salmonella enterica serovar typhimurium. Antimicrob Agents Chemother (2006) 0.90

Mechanisms and fitness costs of tigecycline resistance in Escherichia coli. J Antimicrob Chemother (2013) 0.90

Minor fitness costs in an experimental model of horizontal gene transfer in bacteria. Mol Biol Evol (2014) 0.90

The NudA protein in the gastric pathogen Helicobacter pylori is an ubiquitous and constitutively expressed dinucleoside polyphosphate hydrolase. J Biol Chem (2003) 0.89

Activation of cryptic aminoglycoside resistance in Salmonella enterica. Mol Microbiol (2011) 0.88

Antibiotic treatment in vitro of phenotypically tolerant bacterial populations. J Antimicrob Chemother (2006) 0.87

Error-prone initiation factor 2 mutations reduce the fitness cost of antibiotic resistance. Mol Microbiol (2010) 0.86

Effect of translesion DNA polymerases, endonucleases and RpoS on mutation rates in Salmonella typhimurium. Genetics (2010) 0.86

Translesion DNA polymerases are required for spontaneous deletion formation in Salmonella typhimurium. Proc Natl Acad Sci U S A (2009) 0.85

Amplification of the gene for isoleucyl-tRNA synthetase facilitates adaptation to the fitness cost of mupirocin resistance in Salmonella enterica. Genetics (2010) 0.85

Fitness costs of synonymous mutations in the rpsT gene can be compensated by restoring mRNA base pairing. PLoS One (2013) 0.85

The Origin of Mutants under Selection: Interactions of Mutation, Growth, and Selection. Ecosal Plus (2011) 0.84

Influence of acquired β-lactamases on the evolution of spontaneous carbapenem resistance in Escherichia coli. J Antimicrob Chemother (2012) 0.84

Pathoadaptive mutations in Salmonella enterica isolated after serial passage in mice. PLoS One (2013) 0.82

Compensatory mutations in agrC partly restore fitness in vitro to peptide deformylase inhibitor-resistant Staphylococcus aureus. J Antimicrob Chemother (2012) 0.81

Ribosomes lacking protein S20 are defective in mRNA binding and subunit association. J Mol Biol (2010) 0.81

Lon protease inactivation, or translocation of the lon gene, potentiate bacterial evolution to antibiotic resistance. Mol Microbiol (2013) 0.80

PEG-stabilized lipid disks as carriers for amphiphilic antimicrobial peptides. J Control Release (2011) 0.80

Evolution of broad spectrum β-lactam resistance in an engineered metallo-β-lactamase. J Biol Chem (2012) 0.79

Environmental and genetic modulation of the phenotypic expression of antibiotic resistance. FEMS Microbiol Rev (2017) 0.78

Rebuttal: adaptive mutation in Escherichia coli (Foster). J Bacteriol (2004) 0.76

A multi-type branching model with varying environment for bacterial dynamics with postantibiotic effect. J Theor Biol (2008) 0.76