Live genomics for pathogen monitoring in public health. (Q39092099)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

title

Live genomics for pathogen monitoring in public health (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

0 references

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

Maria Victoria Schneider

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

Andrés Moya

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

author name string

Giuseppe D'Auria

series ordinal

1

1 reference

9 September 2017

21 January 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

volume

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

page(s)

93-108

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

23 February 2020

copyright license

start time

21 January 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

MIRA

object named as

MIRA

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Choosing a benchtop sequencing machine to characterise Helicobacter pylori genomes

1 reference

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Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools

9 September 2017

1 reference

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Overview of molecular typing methods for outbreak detection and epidemiological surveillance.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Procalcitonin predicts real-time PCR results in blood samples from patients with suspected sepsis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Genomic analysis of a key innovation in an experimental Escherichia coli population

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

A beginners guide to SNP calling from high-throughput DNA-sequencing data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Multilocus sequence typing of total-genome-sequenced bacteria

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

PGAP: pan-genomes analysis pipeline

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Bacterial epidemiology and biology - lessons from genome sequencing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

HMMER web server: interactive sequence similarity searching

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Whole-genome sequencing and social-network analysis of a tuberculosis outbreak

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Quality control and preprocessing of metagenomic datasets

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Clinical practice guideline for the use of antimicrobial agents in neutropenic patients with cancer: 2010 update by the infectious diseases society of america

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Antimicrobial Resistance in the Intensive Care Unit: Mechanisms, Epidemiology, and Management of Specific Resistant Pathogens

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

The bacterial pan-genome:a new paradigm in microbiology.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Multiplex blood PCR in combination with blood cultures for improvement of microbiological documentation of infection in febrile neutropenia

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Legionella pneumophila pangenome reveals strain-specific virulence factors.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Evolutionary trajectories of beta-lactamase CTX-M-1 cluster enzymes: predicting antibiotic resistance

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

The Sequence Alignment/Map format and SAMtools

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Comparative genomics: the bacterial pan-genome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Impact of empiric antimicrobial therapy on outcomes in patients with Escherichia coli and Klebsiella pneumoniae bacteremia: a cohort study

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Phylogenetic inference using whole genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Genomic plasticity in prokaryotes: the case of the square haloarchaeon

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Impact of empiric antibiotic therapy on outcomes in patients with Pseudomonas aeruginosa bacteremia

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Bio-banking in microbiology: from sample collection to epidemiology, diagnosis and research

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

9 September 2017

The microbial pan-genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

The impact of methicillin resistance in Staphylococcus aureus bacteremia on patient outcomes: mortality, length of stay, and hospital charges

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Outcome and attributable mortality in critically Ill patients with bacteremia involving methicillin-susceptible and methicillin-resistant Staphylococcus aureus.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Improved microbial gene identification with GLIMMER

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Epidemiology of emerging/re-emerging antimicrobial-resistant bacterial pathogens

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Pfam: multiple sequence alignments and HMM-profiles of protein domains

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Biodiversity: are microbial species threatened?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Clinical and financial benefits of rapid bacterial identification and antimicrobial susceptibility testing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Frequency of Binary Toxin Genes among Clostridium difficile Strains That Do Not Produce Large Clostridial Toxins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Clinical study of an outbreak of Legionnaire's disease in Alcoy, Southeastern Spain

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

An outbreak of multidrug-resistant Serratia marcescens: the importance of continuous monitoring of nosocomial infections

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

A computational genomics pipeline for prokaryotic sequencing projects

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Phylogenetic analyses of phylum Actinobacteria based on whole genome sequences

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

A multiplex real-time PCR assay for rapid detection and differentiation of 25 bacterial and fungal pathogens from whole blood samples

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4235738

Use of Nucleic-Acid Homologies in the Taxonomy of Anaerobic Bacteria

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.3390/PATHOGENS3010093

Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.3390/PATHOGENS3010093

The cost of antibiotic resistance from a bacterial perspective

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25437609

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Molecular epidemiology of human pathogens: how to translate breakthroughs into public health practice, Stockholm, November 2011

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25437609

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3390/PATHOGENS3010093

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

release_yaveczplkbbxxff3fpgug2vpti

23 February 2020

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/yaveczplkbbxxff3fpgug2vpti

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json

23 February 2020

PubMed publication ID

25437609

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25437609 AND SRC:MED&resulttype=core&format=json