Published in BMC Genomics on October 20, 2013
Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak. J Clin Microbiol (2015) 1.08
Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages. Virology (2016) 0.85
Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow. BMC Genomics (2014) 0.82
Differential single nucleotide polymorphism-based analysis of an outbreak caused by Salmonella enterica serovar Manhattan reveals epidemiological details missed by standard pulsed-field gel electrophoresis. J Clin Microbiol (2015) 0.82
Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage. J Clin Microbiol (2015) 0.81
Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing. J Clin Microbiol (2015) 0.79
Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014. BMC Microbiol (2016) 0.75
Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak. BMC Res Notes (2015) 0.75
Evolution of Variable Number Tandem Repeats and Its Relationship with Genomic Diversity in Salmonella Typhimurium. Front Microbiol (2016) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One (2010) 24.31
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
Bacteriophage-typing designations of Salmonella typhimurium. J Hyg (Lond) (1977) 8.59
Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev (2004) 7.93
Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc Natl Acad Sci U S A (2004) 5.98
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res (2009) 3.99
Salmonella typhimurium leucine-rich repeat proteins are targeted to the SPI1 and SPI2 type III secretion systems. Mol Microbiol (1999) 3.15
An alternating least squares approach to inferring phylogenies from pairwise distances. Syst Biol (1997) 2.94
Evolutionary significance of accessory DNA elements in bacteria. Annu Rev Microbiol (1981) 2.75
Inducible prophages contribute to Salmonella virulence in mice. Mol Microbiol (1999) 2.70
Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella. Mol Microbiol (2001) 2.63
Evolution of host adaptation in Salmonella enterica. Infect Immun (1998) 2.57
Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain. Proc Natl Acad Sci U S A (1999) 2.51
Epidemic salmonella typhimurium DT 104--a truly international multiresistant clone. J Antimicrob Chemother (2000) 2.47
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A (2012) 2.39
Biofilm dispersal: mechanisms, clinical implications, and potential therapeutic uses. J Dent Res (2010) 2.29
Identification of host-specific colonization factors of Salmonella enterica serovar Typhimurium. Mol Microbiol (2004) 2.26
Beta-lactam resistance response triggered by inactivation of a nonessential penicillin-binding protein. PLoS Pathog (2009) 2.20
Salmonella enterica serotype Typhimurium and its host-adapted variants. Infect Immun (2002) 2.10
Tissue-specific gene expression identifies a gene in the lysogenic phage Gifsy-1 that affects Salmonella enterica serovar typhimurium survival in Peyer's patches. J Bacteriol (2000) 2.10
An altered rpoS allele contributes to the avirulence of Salmonella typhimurium LT2. Infect Immun (1997) 2.07
The pef fimbrial operon of Salmonella typhimurium mediates adhesion to murine small intestine and is necessary for fluid accumulation in the infant mouse. Infect Immun (1996) 2.04
Recognizing the pseudogenes in bacterial genomes. Nucleic Acids Res (2005) 1.96
The Salmonella typhimurium virulence plasmid complement resistance gene rck is homologous to a family of virulence-related outer membrane protein genes, including pagC and ail. J Bacteriol (1992) 1.89
Nucleotide sequence of a 13.9 kb segment of the 90 kb virulence plasmid of Salmonella typhimurium: the presence of fimbrial biosynthetic genes. Mol Microbiol (1993) 1.89
Identification and characterization of the first class of potent bacterial acetyl-CoA carboxylase inhibitors with antibacterial activity. J Biol Chem (2004) 1.86
Salmonella typhimurium encodes an SdiA homolog, a putative quorum sensor of the LuxR family, that regulates genes on the virulence plasmid. J Bacteriol (1998) 1.85
Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome. J Bacteriol (2009) 1.83
Identification of SopE2, a Salmonella secreted protein which is highly homologous to SopE and involved in bacterial invasion of epithelial cells. J Bacteriol (2000) 1.74
Selection for citrate synthase deficiency in icd mutants of Escherichia coli. J Bacteriol (1976) 1.67
The Salmonella enterica serotype Typhimurium lpf, bcf, stb, stc, std, and sth fimbrial operons are required for intestinal persistence in mice. Infect Immun (2005) 1.66
The inflammation-associated Salmonella SopA is a HECT-like E3 ubiquitin ligase. Mol Microbiol (2006) 1.66
Proteomic analysis of Campylobacter jejuni 11168 biofilms reveals a role for the motility complex in biofilm formation. J Bacteriol (2006) 1.62
The ancestry of insertion sequences common to Escherichia coli and Salmonella typhimurium. J Bacteriol (1993) 1.57
Avirulence of LT2 strains of Salmonella typhimurium results from a defective rpoS gene. Infect Immun (1997) 1.33
Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC Genomics (2009) 1.28
Host adaptation of pigeon isolates of Salmonella enterica subsp. enterica serovar Typhimurium variant Copenhagen phage type 99 is associated with enhanced macrophage cytotoxicity. Infect Immun (2003) 1.27
The SopEPhi phage integrates into the ssrA gene of Salmonella enterica serovar Typhimurium A36 and is closely related to the Fels-2 prophage. J Bacteriol (2003) 1.26
Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms. ISME J (2009) 1.25
Role of the Escherichia coli glgX gene in glycogen metabolism. J Bacteriol (2005) 1.23
Natural populations of Escherichia coli and Salmonella typhimurium harbor the same classes of insertion sequences. Genetics (1993) 1.22
Characterization of the genomes of a diverse collection of Salmonella enterica serovar Typhimurium definitive phage type 104. J Bacteriol (2008) 1.22
The virulence plasmid of Salmonella typhimurium is self-transmissible. J Bacteriol (1999) 1.20
Prokaryotic community composition and ecology of floating macroscopic filaments from an extreme acidic environment, Río Tinto (SW, Spain). Syst Appl Microbiol (2007) 1.20
Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome. Antimicrob Agents Chemother (2010) 1.15
Role in virulence and protective efficacy in pigs of Salmonella enterica serovar Typhimurium secreted components identified by signature-tagged mutagenesis. Microbiology (2007) 1.14
Multiple insertions of fimbrial operons correlate with the evolution of Salmonella serovars responsible for human disease. Mol Microbiol (1999) 1.11
OmpC is the receptor for Gifsy-1 and Gifsy-2 bacteriophages of Salmonella. J Bacteriol (2001) 1.10
Identification of Escherichia coli genes that are specifically expressed in a murine model of septicemic infection. Infect Immun (2002) 1.02
Molecular characterization of a prophage of Salmonella enterica serotype Typhimurium DT104. J Clin Microbiol (2004) 1.01
Host restriction of Salmonella enterica serotype Typhimurium pigeon isolates does not correlate with loss of discrete genes. J Bacteriol (2004) 0.97
Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates. Microbiology (2006) 0.97
Functional characterization of the FimH adhesin from Salmonella enterica serovar Enteritidis. Microbiology (2006) 0.95
Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella enterica Serovar Typhimurium. J Clin Microbiol (2012) 0.93
The NapF protein of the Escherichia coli periplasmic nitrate reductase system: demonstration of a cytoplasmic location and interaction with the catalytic subunit, NapA. Microbiology (2006) 0.92
Salmonella phage ST64B encodes a member of the SseK/NleB effector family. PLoS One (2011) 0.91
Resuscitation of a defective prophage in Salmonella cocultures. J Bacteriol (2004) 0.91
Enhancer-dependent transcription in Salmonella enterica Typhimurium: new members of the sigmaN regulon inferred from protein sequence homology and predicted promoter sites. J Mol Microbiol Biotechnol (2002) 0.87
Adaptation of multilocus sequencing for studying variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium. Genetics (2005) 0.86
Lack of association between long-term illness and infectious intestinal disease in New Zealand. N Z Med J (2004) 0.84
NapF is a cytoplasmic iron-sulfur protein required for Fe-S cluster assembly in the periplasmic nitrate reductase. J Biol Chem (2004) 0.84
Heterogeneity in expression of lipopolysaccharide by strains of Salmonella enterica serotype Typhimurium definitive phage type 104 and related phage types. Lett Appl Microbiol (2002) 0.82
Single nucleotide polymorphism typing of global Salmonella enterica serovar Typhi isolates by use of a hairpin primer real-time PCR assay. J Clin Microbiol (2010) 0.81
Outbreaks of Salmonella Typhimurium phage type 197 of multiple genotypes linked to an egg producer. Commun Dis Intell Q Rep (2009) 0.80
Prevention of HIV-1 infection with early antiretroviral therapy. N Engl J Med (2011) 69.36
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol (2006) 14.53
Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature (2007) 10.94
Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med (2002) 9.70
Integrative molecular concept modeling of prostate cancer progression. Nat Genet (2006) 8.49
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Heterosexual risk of HIV-1 infection per sexual act: systematic review and meta-analysis of observational studies. Lancet Infect Dis (2009) 6.96
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet (2006) 6.43
Regulation of JAK-STAT signalling in the immune system. Nat Rev Immunol (2003) 5.77
Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet (2008) 5.64
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Bipolar transurethral resection of the prostate causes deeper coagulation depth and less bleeding than monopolar transurethral prostatectomy. Urology (2012) 4.61
Endocannabinoid activation at hepatic CB1 receptors stimulates fatty acid synthesis and contributes to diet-induced obesity. J Clin Invest (2005) 4.55
Intravenous administration of human bone marrow stromal cells induces angiogenesis in the ischemic boundary zone after stroke in rats. Circ Res (2003) 4.29
Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial. J Infect Dis (2011) 3.78
Addition of a photocrosslinking amino acid to the genetic code of Escherichiacoli. Proc Natl Acad Sci U S A (2002) 3.77
RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol (2012) 3.72
Statins induce angiogenesis, neurogenesis, and synaptogenesis after stroke. Ann Neurol (2003) 3.54
Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Mod Pathol (2007) 3.37
Complete loss of ischaemic preconditioning-induced cardioprotection in mice with partial deficiency of HIF-1 alpha. Cardiovasc Res (2007) 3.31
Mutant LRRK2(R1441G) BAC transgenic mice recapitulate cardinal features of Parkinson's disease. Nat Neurosci (2009) 3.24
Urbanisation and health in China. Lancet (2012) 3.21
A recalibrated molecular clock and independent origins for the cholera pandemic clones. PLoS One (2008) 3.16
Microglial activation-mediated delayed and progressive degeneration of rat nigral dopaminergic neurons: relevance to Parkinson's disease. J Neurochem (2002) 3.14
Mesenchymal stem cell-based tissue regeneration is governed by recipient T lymphocytes via IFN-γ and TNF-α. Nat Med (2011) 3.11
Regulation of hepcidin transcription by interleukin-1 and interleukin-6. Proc Natl Acad Sci U S A (2005) 3.11
Cost-effectiveness of HIV treatment as prevention in serodiscordant couples. N Engl J Med (2013) 3.10
Characterization of TMPRSS2-ETS gene aberrations in androgen-independent metastatic prostate cancer. Cancer Res (2008) 3.02
Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies susceptibility loci at PLCE1 and C20orf54. Nat Genet (2010) 2.95
Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol (2008) 2.94
NADPH oxidase mediates lipopolysaccharide-induced neurotoxicity and proinflammatory gene expression in activated microglia. J Biol Chem (2003) 2.92
Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A (2008) 2.92
A multicenter observational study of the potential benefits of initiating combination antiretroviral therapy during acute HIV infection. J Infect Dis (2006) 2.88
Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J Am Chem Soc (2002) 2.88
Functional genetic analysis of mouse chromosome 11. Nature (2003) 2.87
A fluorescence in situ hybridization screen for E26 transformation-specific aberrations: identification of DDX5-ETV4 fusion protein in prostate cancer. Cancer Res (2008) 2.87
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res (2006) 2.77
Fluorescence in situ hybridization study shows association of PTEN deletion with ERG rearrangement during prostate cancer progression. Mod Pathol (2009) 2.69
Gliosis and brain remodeling after treatment of stroke in rats with marrow stromal cells. Glia (2005) 2.68
Research resource: Comprehensive expression atlas of the fibroblast growth factor system in adult mouse. Mol Endocrinol (2010) 2.67
Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacteriol (2007) 2.67
Urine TMPRSS2:ERG fusion transcript stratifies prostate cancer risk in men with elevated serum PSA. Sci Transl Med (2011) 2.62
Intravenous bone marrow stromal cell therapy reduces apoptosis and promotes endogenous cell proliferation after stroke in female rat. J Neurosci Res (2003) 2.61
Heterogeneity of TMPRSS2 gene rearrangements in multifocal prostate adenocarcinoma: molecular evidence for an independent group of diseases. Cancer Res (2007) 2.60
Regulation of gene-activation pathways by PIAS proteins in the immune system. Nat Rev Immunol (2005) 2.59
Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Res (2005) 2.57
Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J Bacteriol (2009) 2.51
Clinical, experimental, and genomic differences between intermediately pathogenic, highly pathogenic, and epidemic Streptococcus suis. J Infect Dis (2009) 2.49
Klotho inhibits transforming growth factor-beta1 (TGF-beta1) signaling and suppresses renal fibrosis and cancer metastasis in mice. J Biol Chem (2011) 2.46
Activated neural stem cells contribute to stroke-induced neurogenesis and neuroblast migration toward the infarct boundary in adult rats. J Cereb Blood Flow Metab (2004) 2.41
Noninvasive detection of TMPRSS2:ERG fusion transcripts in the urine of men with prostate cancer. Neoplasia (2006) 2.39
Ischemic rat brain extracts induce human marrow stromal cell growth factor production. Neuropathology (2002) 2.38
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Correlates of HIV acquisition in a cohort of Black men who have sex with men in the United States: HIV prevention trials network (HPTN) 061. PLoS One (2013) 2.32
Nanoparticles modified with tumor-targeting scFv deliver siRNA and miRNA for cancer therapy. Mol Ther (2010) 2.30
Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect (2002) 2.27
Thermal diode: rectification of heat flux. Phys Rev Lett (2004) 2.24
Isolated C-terminal tail of FGF23 alleviates hypophosphatemia by inhibiting FGF23-FGFR-Klotho complex formation. Proc Natl Acad Sci U S A (2009) 2.23
Mesoscopic CH3NH3PbI3/TiO2 heterojunction solar cells. J Am Chem Soc (2012) 2.17
Integrative analysis of genomic aberrations associated with prostate cancer progression. Cancer Res (2007) 2.14
Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature (2007) 2.12
Structure and genetics of Shigella O antigens. FEMS Microbiol Rev (2008) 2.11
A facile synthesis and properties of multicarbazole molecules containing multiple vinylene bridges. J Am Chem Soc (2005) 2.11
Hippocampal deformities in schizophrenia characterized by high dimensional brain mapping. Am J Psychiatry (2002) 2.11
Metabolomic profiling to develop blood biomarkers for Parkinson's disease. Brain (2008) 2.10
(Z)-Ethyl 2,4-diphenyl-3-(propyl-amino)-but-2-enoate. Acta Crystallogr Sect E Struct Rep Online (2009) 2.09
The quality of reporting of randomized controlled trials of traditional Chinese medicine: a survey of 13 randomly selected journals from mainland China. Clin Ther (2007) 2.08
A biosynthetic pathway for anandamide. Proc Natl Acad Sci U S A (2006) 2.08
Streptococcus suis sequence type 7 outbreak, Sichuan, China. Emerg Infect Dis (2006) 2.07
Stromal cell-derived factor 1alpha mediates neural progenitor cell motility after focal cerebral ischemia. J Cereb Blood Flow Metab (2006) 2.06
Simvastatin inhibits smoke-induced airway epithelial injury: implications for COPD therapy. Eur Respir J (2012) 2.06
Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci U S A (2007) 2.06
Silencing threonine deaminase and JAR4 in Nicotiana attenuata impairs jasmonic acid-isoleucine-mediated defenses against Manduca sexta. Plant Cell (2006) 2.05
Plasma cortisol and progression of dementia in subjects with Alzheimer-type dementia. Am J Psychiatry (2006) 2.05
The utility and limitations of glycosylated human CD133 epitopes in defining cancer stem cells. J Mol Med (Berl) (2008) 2.04
A molecular framework of light-controlled phytohormone action in Arabidopsis. Curr Biol (2012) 2.02
Addition of intrarectal local analgesia to periprostatic nerve block improves pain control for transrectal ultrasonography-guided prostate biopsy: a systematic review and meta-analysis. Int J Urol (2014) 2.01
Morbidity and mortality among a cohort of human immunodeficiency virus type 1-infected and uninfected pregnant women and their infants from Malawi, Zambia, and Tanzania. Pediatr Infect Dis J (2008) 2.00
The feasibility of measuring renal blood flow using transesophageal echocardiography in patients undergoing cardiac surgery. Anesth Analg (2009) 1.97
Gene targeting of Cdc42 and Cdc42GAP affirms the critical involvement of Cdc42 in filopodia induction, directed migration, and proliferation in primary mouse embryonic fibroblasts. Mol Biol Cell (2006) 1.96
Thalamic shape abnormalities in individuals with schizophrenia and their nonpsychotic siblings. J Neurosci (2007) 1.95
FreeSurfer-initiated fully-automated subcortical brain segmentation in MRI using Large Deformation Diffeomorphic Metric Mapping. Neuroimage (2008) 1.95
The site-specific incorporation of p-iodo-L-phenylalanine into proteins for structure determination. Nat Biotechnol (2004) 1.93
Suppression of in vitro megakaryocyte production by antiplatelet autoantibodies from adult patients with chronic ITP. Blood (2003) 1.92
Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacteriol (2007) 1.92
Hysteresis in single-layer MoS2 field effect transistors. ACS Nano (2012) 1.92
Correlations between antemortem hippocampal volume and postmortem neuropathology in AD subjects. Alzheimer Dis Assoc Disord (2004) 1.91
Cell type-dependent pro- and anti-inflammatory role of signal transducer and activator of transcription 3 in alcoholic liver injury. Gastroenterology (2008) 1.90
The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data. Brain Imaging Behav (2014) 1.90
Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One (2010) 1.90