Published in Virology on October 25, 2002
Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev (2004) 7.93
Prophage genomics. Microbiol Mol Biol Rev (2003) 4.49
Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom. MBio (2015) 1.54
Genomic organization and molecular characterization of Clostridium difficile bacteriophage PhiCD119. J Bacteriol (2006) 1.51
Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis. BMC Genomics (2009) 1.32
Phage-associated mutator phenotype in group A streptococcus. J Bacteriol (2008) 1.21
Phage Therapy - Everything Old is New Again. Can J Infect Dis Med Microbiol (2006) 1.17
Bacteriophage-mediated toxin gene regulation in Clostridium difficile. J Virol (2009) 1.09
A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nat Rev Microbiol (2015) 1.03
Permanent genetic memory with >1-byte capacity. Nat Methods (2014) 1.00
Molecular epidemiology and genomics of group A Streptococcus. Infect Genet Evol (2014) 1.00
Functional analysis of the quorum-sensing streptococcal invasion locus (sil). PLoS Pathog (2009) 0.99
New genetic element carrying the erythromycin resistance determinant erm(TR) in Streptococcus pneumoniae. Antimicrob Agents Chemother (2007) 0.97
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Prophagic DNA fragments in Streptococcus agalactiae strains and association with neonatal meningitis. J Clin Microbiol (2006) 0.92
Cultivation-based assessment of lysogeny among soil bacteria. Microb Ecol (2008) 0.87
Phage-Like Streptococcus pyogenes Chromosomal Islands (SpyCI) and Mutator Phenotypes: Control by Growth State and Rescue by a SpyCI-Encoded Promoter. Front Microbiol (2012) 0.86
Elimination of Chromosomal Island SpyCIM1 from Streptococcus pyogenes Strain SF370 Reverses the Mutator Phenotype and Alters Global Transcription. PLoS One (2015) 0.84
Chromosomal islands of Streptococcus pyogenes and related streptococci: molecular switches for survival and virulence. Front Cell Infect Microbiol (2014) 0.84
Novel algorithms reveal streptococcal transcriptomes and clues about undefined genes. PLoS Comput Biol (2007) 0.83
Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors. BMC Genomics (2015) 0.82
In vivo lysogenization of a Clostridium difficile bacteriophage ФCD119. Anaerobe (2011) 0.81
The structural characterization of a prophage-encoded extracellular DNase from Streptococcus pyogenes. Nucleic Acids Res (2011) 0.78
The prophage-encoded hyaluronate lyase has broad substrate specificity and is regulated by the N-terminal domain. J Biol Chem (2014) 0.77
Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome. BMC Microbiol (2011) 0.77
Comparison and optimization of ten phage encoded serine integrases for genome engineering in Saccharomyces cerevisiae. BMC Biotechnol (2016) 0.76
A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Nucleic Acids Res (2015) 0.76
Targeted Curing of All Lysogenic Bacteriophage from Streptococcus pyogenes Using a Novel Counter-selection Technique. PLoS One (2016) 0.75
Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps. Sci Rep (2016) 0.75
Logic Synthesis of Recombinase-Based Genetic Circuits. Sci Rep (2017) 0.75
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Enterotypes of the human gut microbiome. Nature (2011) 24.36
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34
Prepublication data sharing. Nature (2009) 12.24
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17
Rapid pneumococcal evolution in response to clinical interventions. Science (2011) 9.09
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95
Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci U S A (2002) 8.25
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet (2006) 8.02
Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc Natl Acad Sci U S A (2004) 7.30
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A (2002) 7.21
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis (2012) 7.18
The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S A (2003) 6.79
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis (2012) 6.64
Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet (2006) 6.43
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med (2012) 6.36
GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30
Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis (2011) 6.08
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi. J Bacteriol (2007) 5.88
Evidence for several waves of global transmission in the seventh cholera pandemic. Nature (2011) 5.62
DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49
Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J (2010) 5.43
Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A (2004) 5.04
Microbiology in the post-genomic era. Nat Rev Microbiol (2008) 4.88
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet (2013) 4.75
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
Prophage genomics. Microbiol Mol Biol Rev (2003) 4.49
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol (2014) 4.39
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics (2006) 4.27
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res (2009) 4.12
Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet (2012) 4.10
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res (2009) 3.99
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet (2013) 3.89
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci U S A (2004) 3.88
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol (2008) 3.85
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog (2012) 3.81
Genome plasticity of BCG and impact on vaccine efficacy. Proc Natl Acad Sci U S A (2007) 3.73
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol (2009) 3.66
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63
Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol (2007) 3.62
Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res (2008) 3.54
Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res (2007) 3.45
Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun (2009) 3.36
Comparative genomic structure of prokaryotes. Annu Rev Genet (2004) 3.34
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet (2006) 3.33
Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet (2003) 3.30
Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res (2008) 3.26
BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics (2010) 3.24
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet (2012) 3.22
Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A (2010) 3.18
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol (2011) 3.11
Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol (2008) 3.10
Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science (2005) 3.08
Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res (2008) 3.03
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet (2013) 3.03
Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol (2002) 3.02
The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol (2006) 2.93
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet (2009) 2.87
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet (2012) 2.86
Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science (2005) 2.86
Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW). J Bacteriol (2009) 2.81
Microevolution of extensively drug-resistant tuberculosis in Russia. Genome Res (2012) 2.81
The impact of prophages on bacterial chromosomes. Mol Microbiol (2004) 2.72
The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol (2008) 2.71
Phage as agents of lateral gene transfer. Curr Opin Microbiol (2003) 2.68
Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome Res (2007) 2.67
Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med (2013) 2.63
Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet (2013) 2.63
A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination? Genome Res (2006) 2.62
Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science (2002) 2.62
A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res (2013) 2.59
Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli. Mol Microbiol (2006) 2.58
Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J (2010) 2.55
Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med (2013) 2.52
Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81. J Bacteriol (2008) 2.51
Phage-host interaction: an ecological perspective. J Bacteriol (2004) 2.50
Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. J Bacteriol (2003) 2.50
Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18. PLoS Genet (2006) 2.47
Wolbachia variability and host effects on crossing type in Culex mosquitoes. Nature (2005) 2.47
Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. J Bacteriol (2008) 2.47
The role of prophage-like elements in the diversity of Salmonella enterica serovars. J Mol Biol (2004) 2.45
Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet (2012) 2.44
Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci U S A (2006) 2.43
Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. PLoS One (2009) 2.38
The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics. Plasmid (2004) 2.36
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics (2007) 2.31
Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates. Genome Res (2007) 2.29
Human volunteers receiving Escherichia coli phage T4 orally: a safety test of phage therapy. Antimicrob Agents Chemother (2005) 2.28
Genome evolution of Wolbachia strain wPip from the Culex pipiens group. Mol Biol Evol (2008) 2.26
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. israelensis. Appl Environ Microbiol (2002) 2.18
Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia. PLoS Negl Trop Dis (2010) 2.17
The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation. Genome Res (2005) 2.12
A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J Bacteriol (2010) 2.08