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ITEP: an integrated toolkit for exploration of microbial pan-genomes
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scholarly article
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Europe PubMed Central
PubMed publication ID
24387194
retrieved
6 August 2017
title
ITEP: an integrated toolkit for exploration of microbial pan-genomes
(English)
1 reference
stated in
Europe PubMed Central
PubMed publication ID
24387194
retrieved
6 August 2017
author
Nathan D Price
series ordinal
5
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Europe PubMed Central
PMC publication ID
3890548
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
retrieved
13 June 2020
author name string
Matthew N Benedict
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1
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Europe PubMed Central
PMC publication ID
3890548
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
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13 June 2020
James R Henriksen
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2
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Europe PubMed Central
PMC publication ID
3890548
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
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13 June 2020
William W Metcalf
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3
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3890548
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13 June 2020
Rachel J Whitaker
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4
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3890548
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13 June 2020
language of work or name
English
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publication date
3 January 2014
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Europe PubMed Central
PubMed publication ID
24387194
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6 August 2017
published in
BMC Genomics
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Europe PubMed Central
PMC publication ID
3890548
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
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13 June 2020
volume
15
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Europe PubMed Central
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3890548
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
retrieved
13 June 2020
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8
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13 June 2020
cites work
Clustering evolving proteins into homologous families
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Coral: an integrated suite of visualizations for comparing clusterings
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Toward community standards in the quest for orthologs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
GenBank
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
PGAP: pan-genomes analysis pipeline
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Computational methods for Gene Orthology inference
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The Salmonella enterica pan-genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
A decade's perspective on DNA sequencing technology
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
OrthoInspector: comprehensive orthology analysis and visual exploration
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Genome-wide comparative gene family classification
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The bacterial pan-genome:a new paradigm in microbiology.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
High-throughput generation, optimization and analysis of genome-scale metabolic models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
QIIME allows analysis of high-throughput community sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
FastTree 2--approximately maximum-likelihood trees for large alignments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
ETE: a python Environment for Tree Exploration
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
A protocol for generating a high-quality genome-scale metabolic reconstruction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Genomics. Genome project standards in a new era of sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Biogeography of the Sulfolobus islandicus pan-genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Biopython: freely available Python tools for computational molecular biology and bioinformatics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Phylogenetic and functional assessment of orthologs inference projects and methods
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Genome-scale models of bacterial metabolism: reconstruction and applications
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The quest for orthologs: finding the corresponding gene across genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
JCoast - a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The RAST Server: rapid annotations using subsystems technology
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Orthologs, paralogs, and evolutionary genomics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Examining bacterial species under the specter of gene transfer and exchange
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
An efficient algorithm for large-scale detection of protein families
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
STRAP: editor for STRuctural Alignments of Proteins
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The use of gene clusters to infer functional coupling
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Measuring genome evolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Basic local alignment search tool
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
8 July 2018
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
27 September 2018
Family specific rates of protein evolution.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
27 September 2018
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3890548
retrieved
27 September 2018
Identifiers
DOI
10.1186/1471-2164-15-8
1 reference
stated in
Europe PubMed Central
PMC publication ID
3890548
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
retrieved
13 June 2020
PMC publication ID
3890548
1 reference
stated in
Europe PubMed Central
PMC publication ID
3890548
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
retrieved
13 June 2020
PubMed publication ID
24387194
1 reference
stated in
Europe PubMed Central
PMC publication ID
3890548
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24387194%20AND%20SRC:MED&resulttype=core&format=json
retrieved
13 June 2020
ResearchGate publication ID
259585555
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