Bacterial strain typing in the genomic era. (Q30377265)

21 June 2017

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title

Bacterial strain typing in the genomic era. (English)

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21 June 2017

2

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21 June 2017

Pierre-Édouard Fournier

series ordinal

3

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author name string

Wenjun Li

series ordinal

1

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21 June 2017

publication date

6 May 2009

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FEMS Microbiology Reviews

21 June 2017

published in

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21 June 2017

volume

33

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21 June 2017

issue

5

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21 June 2017

page(s)

892-916

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The multilocus sequence typing network: mlst.net

21 June 2017

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Nucleotide sequence-based typing of bacteria and the impact of automation

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Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications

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Evaluation of Pulsed-Field Gel Electrophoresis as a Tool for Determining the Degree of Genetic Relatedness between Strains of Escherichia coli O157:H7

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Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants

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The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

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The molecular evolution of methicillin-resistant Staphylococcus aureus

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Genotypic characterization of Neisseria meningitidis using Pyrosequencing

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Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity.

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Genotyping, Orientalis-like Yersinia pestis, and plague pandemics

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Uses of Staphylococcus aureus GeneChips in genotyping and genetic composition analysis

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Diversity of the human intestinal microbial flora

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A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease

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Genotyping of Mycoplasma gallisepticum and M. synoviae by Amplified Fragment Length Polymorphism (AFLP) analysis and digitalized Random Amplified Polymorphic DNA (RAPD) analysis.

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Recombination and the population structures of bacterial pathogens

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Performance assessment of DNA fragment sizing by high-sensitivity flow cytometry and pulsed-field gel electrophoresis

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Multispacer typing technique for sequence-based typing of Bartonella quintana

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Phylogenetic analysis of spotted fever group rickettsiae by study of the outer surface protein rOmpA

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Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains

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Insights on biology and evolution from microbial genome sequencing

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Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

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DNA microarray-based typing of an atypical monophasic Salmonella enterica serovar

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DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens?

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PulseNet USA: a five-year update

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Coxiella burnetii genotyping

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On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing

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Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method

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New Staphylococcus aureus genotyping method based on exotoxin (set) genes

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Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes

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New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region

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Resequencing and mutational analysis using oligonucleotide microarrays

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Advanced sequencing technologies and their wider impact in microbiology

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Validation of pulsed-field gel electrophoresis and spa typing for long-term, nationwide epidemiological surveillance studies of Staphylococcus aureus infections

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Restriction fragment length polymorphism typing of Mycobacterium tuberculosis

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Typing of mycobacteria using spoligotyping

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Microbial DNA typing by automated repetitive-sequence-based PCR.

21 January 2018

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Pulsed-field gel electrophoresis

21 January 2018

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Pulmonary tuberculosis in Harare, Zimbabwe: analysis by spoligotyping.

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Evidence for biased gene conversion in concerted evolution of ribosomal DNA.

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Capillary electrophoretic restriction fragment length polymorphism patterns for the Mycobacterial hsp65 gene

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Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States

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16S/23S rRNA intergenic spacer regions for phylogenetic analysis, identification, and subtyping of Bartonella species

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ERIC sequences: a novel family of repetitive elements in the genomes ofEscherichia coli, Salmonella typhimuriumand other enterobacteria

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Genomic sequencing of single microbial cells from environmental samples

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Classification of Mycoplasma synoviae strains using single-strand conformation polymorphism and high-resolution melting-curve analysis of the vlhA gene single-copy region

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Direct detection of multidrug-resistant Mycobacterium tuberculosis in clinical specimens in low- and high-incidence countries by line probe assay

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Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis

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mlstdbNet - distributed multi-locus sequence typing (MLST) databases

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Rapid detection of rifampin resistance in Mycobacterium tuberculosis by Pyrosequencing technology

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Molecular methods for Mycobacterium tuberculosis strain typing: a users guide

21 January 2018

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Clostridium difficile genotyping based on slpA variable region in S-layer gene sequence: an alternative to serotyping

21 January 2018

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Typing by sequencing the slpA gene of Clostridium difficile strains causing multiple outbreaks in Japan

21 January 2018

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Comparing genomes within the species Mycobacterium tuberculosis

21 January 2018

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Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis

21 January 2018

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Exploring the unknown. The silent revolution of microbiology

21 January 2018

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DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli

21 January 2018

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Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution

21 January 2018

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Optimization of cDNA-AFLP experiments using genomic sequence data

21 January 2018

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Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome

21 January 2018

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Intraspecific variation in the 16S rRNA gene sequences of Mycoplasma agalactiae and Mycoplasma bovis strains

21 January 2018

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spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation

21 January 2018

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Double-locus sequence typing using clfB and spa, a fast and simple method for epidemiological typing of methicillin-resistant Staphylococcus aureus.

21 January 2018

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Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensis paradigm

21 January 2018

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High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing

21 January 2018

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Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

21 January 2018

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Sequence-based estimation of minisatellite and microsatellite repeat variability

21 January 2018

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A new method for RAPD primers selection based on primer bias in nucleotide sequence data

21 January 2018

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Multispacer typing to study the genotypic distribution of Bartonella henselae populations.

21 January 2018

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Genetic diversity of Bartonella henselae in human infection detected with multispacer typing

21 January 2018

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Genotyping reveals a wide heterogeneity of Tropheryma whipplei.

21 January 2018

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Use of a multilocus variable-number tandem repeat analysis method for molecular subtyping and phylogenetic analysis of Neisseria meningitidis isolates

21 January 2018

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Combination of competitive quantitative PCR and constant-denaturant capillary electrophoresis for high-resolution detection and enumeration of microbial cells

21 January 2018

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Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria.

21 January 2018

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Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis

21 January 2018

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Escherichia coli O antigen typing using DNA microarrays.

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Introduction to the polymerase chain reaction

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Expression monitoring by hybridization to high-density oligonucleotide arrays

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Microarrays for microbiologists

21 January 2018

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Short, interspersed repetitive DNA sequences in prokaryotic genomes.

21 January 2018

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Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

21 January 2018

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Genome sequencing in microfabricated high-density picolitre reactors

21 January 2018

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The use of (GTG)5 oligonucleotide as an RAPD primer to type Campylobacter concisus

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21 January 2018

The microbial pan-genome

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The Genome Sequence of Mycoplasma hyopneumoniae Strain 232, the Agent of Swine Mycoplasmosis

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Applications of DNA tiling arrays for whole-genome analysis

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rpoB sequence analysis as a novel basis for bacterial identification

21 January 2018

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Are variable-number tandem repeats appropriate for genotyping Mycobacterium leprae?

21 January 2018

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Methods used in the molecular epidemiology of tuberculosis.

21 January 2018

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AFLP genotyping and fingerprinting

21 January 2018

1 reference

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Selfish DNA in Protein-Coding Genes of Rickettsia

21 January 2018

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RAPD typing in microbiology--a technical review

21 January 2018

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High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni.

21 January 2018

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The Uncultured Microbial Majority

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Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet

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A sequencing method based on real-time pyrophosphate

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Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections

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Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination

21 January 2018

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Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool

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The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains.

21 January 2018

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DNA Sequencing Techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

DNA sequencing with chain-terminating inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Single nucleotide polymorphisms and the future of genetic epidemiology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Clinical evaluation of the DiversiLab microbial typing system using repetitive-sequence-based PCR for characterization of Staphylococcus aureus strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Changes in size and secondary structure of the ribosomal transcription unit during vertebrate evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Repetitive extragenic palindromic sequences: a major component of the bacterial genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Building PulseNet International: an interconnected system of laboratory networks to facilitate timely public health recognition and response to foodborne disease outbreaks and emerging foodborne diseases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Multiple-locus variable-number tandem-repeat assay analysis of methicillin-resistant Staphylococcus aureus strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Diversity and dynamics of a north atlantic coastal Vibrio community.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

From the chromosome to DNA: Restriction fragment length polymorphism analysis and its clinical application

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

DNA macroarray for identification and typing of Staphylococcus aureus isolates

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Molecular typing of Neisseria gonorrhoeae isolates by pyrosequencing of highly polymorphic segments of the porB gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA).

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Typing and subtyping of Clostridium difficile isolates by using multiple-locus variable-number tandem-repeat analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Minisatellites: mutability and genome architecture.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

AFLP: a new technique for DNA fingerprinting

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Pyrosequencing Bacillus anthracis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Fingerprinting genomes using PCR with arbitrary primers

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

The current MLVA typing scheme for Enterococcus faecium is less discriminatory than MLST and PFGE for epidemic-virulent, hospital-adapted clonal types

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Rapid molecular typing of methicillin-resistant Staphylococcus aureus by PCR-RFLP.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

DNA polymorphisms amplified by arbitrary primers are useful as genetic markers

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Model-P: a basecalling method for resequencing microarrays of diploid samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

A novel genotypic test for rapid detection of multidrug-resistant Mycobacterium tuberculosis isolates by a multiplex probe array

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Microarrays for bacterial detection and microbial community analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Multispacer typing of Rickettsia prowazekii enabling epidemiological studies of epidemic typhus

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

FluoMEP: A new genotyping method combining the advantages of randomly amplified polymorphic DNA and amplified fragment length polymorphism

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Optimization of High-Resolution Melting Analysis for Low-Cost and Rapid Screening of Allelic Variants of Bacillus anthracis by Multiple-Locus Variable-Number Tandem Repeat Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

AFLPinSilico, simulating AFLP fingerprints

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

Use of the 16S–23S ribosomal genes spacer region in studies of prokaryotic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111/J.1574-6976.2009.00182.X

10.1111/J.1574-6976.2009.00182.X

21 January 2018

Identifiers

DOI

1 reference

21 June 2017

1 reference