(Q24247657)

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Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27107716%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27107716%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Promoter prediction

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transcription start site

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Bradyrhizobium japonicum

1 reference

based on heuristic

inferred from title

Jelena Čuklina

1

1 reference

Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27107716%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Konrad Förstner

5

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2 April 2020

Gabriella Pessi

8

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2 April 2020

Christian H. Ahrens

10

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2 April 2020

Mikhail Gelfand

11

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2 April 2020

author name string

Julia Hahn

2

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2 April 2020

Maxim Imakaev

3

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2 April 2020

Ulrich Omasits

4

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2 April 2020

Nikolay Ljubimov

6

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2 April 2020

Melanie Goebel

7

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2 April 2020

Hans-Martin Fischer

9

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2 April 2020

Elena Evguenieva-Hackenberg

12

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2 April 2020

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23 April 2016

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2 April 2020

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2 April 2020

17

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2 April 2020

1

0 references

302

1 reference

Europe PubMed Central

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2 April 2020

describes a project that uses

1 reference

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19 March 2017

Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli

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19 March 2017

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19 March 2017

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19 March 2017

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19 March 2017

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19 March 2017

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19 March 2017

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19 March 2017

Complete Genomic Sequence of Nitrogen-fixing Symbiotic Bacterium Bradyrhizobium japonicum USDA110

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19 March 2017

Proteogenomics: concepts, applications and computational strategies

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19 March 2017

Prodigal: prokaryotic gene recognition and translation initiation site identification

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7 April 2017

Bacterial RNA polymerase can retain σ70 throughout transcription.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli

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27 September 2017

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27 September 2017

Conservation of transcription start sites within genes across a bacterial genus

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27 September 2017

A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

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27 September 2017

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline

1 reference

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27 September 2017

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

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27 September 2017

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021.

1 reference

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27 September 2017

Reactive oxygen species-inducible ECF σ factors of Bradyrhizobium japonicum

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27 September 2017

Dual RNA-seq of pathogen and host

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27 September 2017

Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium

1 reference

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27 September 2017

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

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27 September 2017

ProOpDB: Prokaryotic Operon DataBase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Root nodulation: a paradigm for how plant-microbe symbiosis influences host developmental pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Generating and navigating proteome maps using mass spectrometry.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Proteogenomics to discover the full coding content of genomes: a computational perspective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Protein and gene model inference based on statistical modeling in k-partite graphs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Missing genes in the annotation of prokaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Dissection of the Bradyrhizobium japonicum NifA+sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Global protein expression pattern of Bradyrhizobium japonicum bacteroids: a prelude to functional proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Bacterial ribosomal RNA in pieces

1 reference

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27 September 2017

Genetic regulation of biological nitrogen fixation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

The Bradyrhizobium japonicum nolA gene encodes three functionally distinct proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Bradyrhizobium japonicum FixK2, a crucial distributor in the FixLJ-dependent regulatory cascade for control of genes inducible by low oxygen levels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Expression of the fixR-nifA operon in Bradyrhizobium japonicum depends on a new response regulator, RegR.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Dissection of the transcription machinery for housekeeping genes of Bradyrhizobium japonicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Genetic regulation of nitrogen fixation in rhizobia.

1 reference

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27 September 2017

A consensus promoter sequence for Caulobacter crescentus genes involved in biosynthetic and housekeeping functions

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27 September 2017

Rhizobium japonicum nitrogenase Fe protein gene (nifH)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Activation of the Bradyrhizobium japonicum nifH and nifDK operons is dependent on promoter-upstream DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Role of the Bradyrhizobium japonicum ntrC gene product in differential regulation of the glutamine synthetase II gene (glnII).

1 reference

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27 September 2017

Differential transcription of the two glutamine synthetase genes of Bradyrhizobium japonicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

27 September 2017

Bradyrhizobium japonicum has two differentially regulated, functional homologs of the sigma 54 gene (rpoN).

1 reference

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27 September 2017

The Bradyrhizobium japonicum nolA gene and its involvement in the genotype-specific nodulation of soybeans

1 reference

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27 September 2017

Expression of regulatory nif genes in Rhodobacter capsulatus

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27 September 2017

Differential RNA-seq: the approach behind and the biological insight gained

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30 May 2018

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

1 reference

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30 May 2018

High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala

1 reference

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30 May 2018

Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli.

1 reference

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30 May 2018

Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage phiYS40.

1 reference

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30 May 2018

The pleiotropic nature of symbiotic regulatory mutants: Bradyrhizobium japonicum nifA gene is involved in control of nif gene expression and formation of determinate symbiosis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

30 May 2018

Three disparately regulated genes for sigma 32-like transcription factors in Bradyrhizobium japonicum.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842269

30 May 2018

A comparative proteomic evaluation of culture grown vs nodule isolated Bradyrhizobium japonicum.

1 reference

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21 January 2018

The PhyR-sigma(EcfG) signalling cascade is involved in stress response and symbiotic efficiency in Bradyrhizobium japonicum.

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

Expression of the Bradyrhizobium japonicum type III secretion system in legume nodules and analysis of the associated tts box promoter.

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

The excludon: a new concept in bacterial antisense RNA-mediated gene regulation

1 reference

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21 January 2018

Positive regulation of psbA gene expression by cis-encoded antisense RNAs in Synechocystis sp. PCC 6803.

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

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https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

The Rhizobium etli gene iscN is highly expressed in bacteroids and required for nitrogen fixation

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

RNA polymerase from Rhizobium japonicum.

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

ARNold: a web tool for the prediction of Rho-independent transcription terminators.

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21 January 2018

An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum

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21 January 2018

ZIC-cHILIC as a fractionation method for sensitive and powerful shotgun proteomics

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21 January 2018

Small RNAs of theBradyrhizobium/Rhodopseudomonaslineage and their analysis

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

Genome-Wide Transcript Analysis ofBradyrhizobium japonicumBacteroids in Soybean Root Nodules

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2602-9

21 January 2018

Transposon-induced symbiotic mutants of Bradyrhizobium japonicum: isolation of two gene regions essential for nodulation

1 reference

https://pubmed.ncbi.nlm.nih.gov/27107716

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulation of nod gene expression in Bradyrhizobium japonicum

1 reference

https://pubmed.ncbi.nlm.nih.gov/27107716

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An Ergatis-based prokaryotic genome annotation web server

1 reference

https://pubmed.ncbi.nlm.nih.gov/27107716

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis

1 reference

https://pubmed.ncbi.nlm.nih.gov/27107716

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PeptideClassifier for protein inference and targeted quantitative proteomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/27107716

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A Comparative Transcriptome Analysis ofRhizobium etliBacteroids: Specific Gene Expression During Symbiotic Nongrowth

1 reference

https://pubmed.ncbi.nlm.nih.gov/27107716

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A role for Bradyrhizobium japonicum ECF16 sigma factor EcfS in the formation of a functional symbiosis with soybean

1 reference

https://pubmed.ncbi.nlm.nih.gov/27107716

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/S12864-016-2602-9

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27107716%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Dimensions Publication ID

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/s12864-016-2602-9

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27107716%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

PubMed publication ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27107716%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

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