Published in MBio on April 11, 2017
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) (2012) 20.08
BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics (2010) 9.30
Predicting the functional effect of amino acid substitutions and indels. PLoS One (2012) 8.61
Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J Clin Microbiol (2003) 7.38
The epidemiology and clinical spectrum of melioidosis: 540 cases from the 20 year Darwin prospective study. PLoS Negl Trop Dis (2010) 7.07
Melioidosis. N Engl J Med (2012) 6.94
NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res (2016) 5.40
Cystic fibrosis. Lancet (2009) 5.40
The bacterial cell envelope. Cold Spring Harb Perspect Biol (2010) 5.14
Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat Genet (2011) 4.81
Efflux-mediated aminoglycoside and macrolide resistance in Burkholderia pseudomallei. Antimicrob Agents Chemother (1999) 4.29
Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci U S A (2004) 4.13
Membrane lipid homeostasis in bacteria. Nat Rev Microbiol (2008) 3.88
Short-chain dehydrogenases/reductases (SDR): the 2002 update. Chem Biol Interact (2003) 3.46
DNA mismatch repair: molecular mechanisms and biological function. Annu Rev Microbiol (2003) 3.42
Development and evaluation of a real-time PCR assay targeting the type III secretion system of Burkholderia pseudomallei. J Clin Microbiol (2006) 2.94
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol (2009) 2.94
Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet (2011) 2.86
PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res (2004) 2.76
Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat Genet (2013) 2.59
Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology. J Bacteriol (2005) 2.59
Melioidosis: an important cause of pneumonia in residents of and travellers returned from endemic regions. Eur Respir J (2003) 2.51
The type II O-antigenic polysaccharide moiety of Burkholderia pseudomallei lipopolysaccharide is required for serum resistance and virulence. Mol Microbiol (1998) 2.46
Insights into the evolutionary process of genome degradation. Curr Opin Genet Dev (1999) 2.25
Clinical significance of microbial infection and adaptation in cystic fibrosis. Clin Microbiol Rev (2011) 2.23
The cluster 1 type VI secretion system is a major virulence determinant in Burkholderia pseudomallei. Infect Immun (2011) 2.00
Type III secretion system cluster 3 is required for maximal virulence of Burkholderia pseudomallei in a hamster infection model. FEMS Microbiol Lett (2005) 1.89
Directed mutagenesis of dihydrofolate reductase. Science (1983) 1.88
Auxotrophic variants of Pseudomonas aeruginosa are selected from prototrophic wild-type strains in respiratory infections in patients with cystic fibrosis. J Clin Microbiol (1995) 1.87
Melioidosis: evolving concepts in epidemiology, pathogenesis, and treatment. Semin Respir Crit Care Med (2015) 1.76
A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-Amino-4-deoxy-L-arabinose. Identification and function oF UDP-4-deoxy-4-formamido-L-arabinose. J Biol Chem (2005) 1.66
Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection. MBio (2013) 1.66
A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog (2010) 1.65
Genetic architecture of intrinsic antibiotic susceptibility. PLoS One (2009) 1.61
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol (2016) 1.54
Mechanisms of antibiotic resistance in Burkholderia pseudomallei: implications for treatment of melioidosis. Future Microbiol (2012) 1.52
Predicted global distribution of Burkholderia pseudomallei and burden of melioidosis. Nat Microbiol (2016) 1.51
Burkholderia pseudomallei: another emerging pathogen in cystic fibrosis. Thorax (2003) 1.50
A mutant of Burkholderia pseudomallei, auxotrophic in the branched chain amino acid biosynthetic pathway, is attenuated and protective in a murine model of melioidosis. Infect Immun (2002) 1.45
Evolution of Burkholderia pseudomallei in recurrent melioidosis. PLoS One (2012) 1.43
Cystic Fibrosis and Burkholderia pseudomallei Infection: An Emerging Problem? Clin Infect Dis (2002) 1.35
Method for regulated expression of single-copy efflux pump genes in a surrogate Pseudomonas aeruginosa strain: identification of the BpeEF-OprC chloramphenicol and trimethoprim efflux pump of Burkholderia pseudomallei 1026b. Antimicrob Agents Chemother (2006) 1.33
Antimicrobial resistance to ceftazidime involving loss of penicillin-binding protein 3 in Burkholderia pseudomallei. Proc Natl Acad Sci U S A (2011) 1.29
Pseudomonas aeruginosa exploits lipid A and muropeptides modification as a strategy to lower innate immunity during cystic fibrosis lung infection. PLoS One (2009) 1.26
Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol Evol (2010) 1.24
Using BOX-PCR to exclude a clonal outbreak of melioidosis. BMC Infect Dis (2007) 1.24
Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa. PLoS Genet (2012) 1.20
SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets. BMC Res Notes (2014) 1.16
Environmental heterogeneity drives within-host diversification and evolution of Pseudomonas aeruginosa. MBio (2014) 1.16
Burkholderia pseudomallei type G in Western Hemisphere. Emerg Infect Dis (2014) 1.13
Immunogenic Burkholderia pseudomallei outer membrane proteins as potential candidate vaccine targets. PLoS One (2009) 1.10
Comparative genomics of isolates of a Pseudomonas aeruginosa epidemic strain associated with chronic lung infections of cystic fibrosis patients. PLoS One (2014) 1.09
Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients' airways and antimicrobial therapy. PLoS One (2011) 1.09
Adaptation of Staphylococcus aureus to the cystic fibrosis lung. Int J Med Microbiol (2010) 1.08
Regulation of type VI secretion system during Burkholderia pseudomallei infection. Infect Immun (2011) 1.07
Characterization of ceftazidime resistance mechanisms in clinical isolates of Burkholderia pseudomallei from Australia. PLoS One (2012) 1.07
Development of ceftazidime resistance in an acute Burkholderia pseudomallei infection. Infect Drug Resist (2012) 1.06
The OmpA family of proteins: roles in bacterial pathogenesis and immunity. Vet Microbiol (2012) 1.02
Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection. mSystems (2016) 1.01
ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics (2015) 1.00
Bandage: interactive visualization of de novo genome assemblies. Bioinformatics (2015) 0.99
High-level resistance to fluoroquinolones and cephalosporins in Burkholderia pseudomallei and closely related species. Trans R Soc Trop Med Hyg (2008) 0.98
Directed evolution of trimethoprim resistance in Escherichia coli. FEBS J (2007) 0.96
Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts. BMC Genomics (2006) 0.95
Whole-genome sequencing of Burkholderia pseudomallei isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type. J Clin Microbiol (2014) 0.95
Burkholderia cenocepacia phenotypic clonal variation during a 3.5-year colonization in the lungs of a cystic fibrosis patient. Infect Immun (2011) 0.94
FolM, a new chromosomally encoded dihydrofolate reductase in Escherichia coli. J Bacteriol (2003) 0.94
Microevolution of Burkholderia pseudomallei during an acute infection. J Clin Microbiol (2014) 0.92
Management of refractory Pseudomonas aeruginosa infection in cystic fibrosis. Infect Drug Resist (2011) 0.90
Hypermutation in Burkholderia cepacia complex is mediated by DNA mismatch repair inactivation and is highly prevalent in cystic fibrosis chronic respiratory infection. Int J Med Microbiol (2014) 0.84
Whole-Genome Sequences of Five Burkholderia pseudomallei Isolates from Australian Cystic Fibrosis Patients. Genome Announc (2015) 0.81
The tandem repeats enabling reversible switching between the two phases of β-lactamase substrate spectrum. PLoS Genet (2014) 0.81
Burkholderia pseudomallei in cystic fibrosis and treatment complications. Respirol Case Rep (2014) 0.81
Finished Annotated Genome Sequence of Burkholderia pseudomallei Strain Bp1651, a Multidrug-Resistant Clinical Isolate. Genome Announc (2015) 0.80
Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply. J Clin Microbiol (2015) 0.80
Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity. Microb Genom (2016) 0.77
Sphingosine-1-phosphate signaling: unraveling its role as a drug target against infectious diseases. Drug Discov Today (2015) 0.76
An international, multicentre evaluation and description of Burkholderia pseudomallei infection in cystic fibrosis. BMC Pulm Med (2015) 0.76
Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility. Genome Announc (2017) 0.76
Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy. J Clin Microbiol (2014) 1.05
Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei. Genome Announc (2015) 0.96
Whole-genome sequencing of Burkholderia pseudomallei isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type. J Clin Microbiol (2014) 0.95
Whole-Genome Sequences of Five Burkholderia pseudomallei Isolates from Australian Cystic Fibrosis Patients. Genome Announc (2015) 0.81
Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply. J Clin Microbiol (2015) 0.80
Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility. Genome Announc (2017) 0.76
Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis. PLoS Negl Trop Dis (2017) 0.75
Mechanisms of Resistance to Folate Pathway Inhibitors in Burkholderia pseudomallei: Deviation from the Norm. MBio (2017) 0.75
Loss of methyltransferase function and increased efflux activity leads to doxycycline resistance in Burkholderia pseudomallei. Antimicrob Agents Chemother (2017) 0.75