(Q56890466)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

title

Pan-cancer deconvolution of tumour composition using DNA methylation (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

0 references

1 reference

corrigendum / erratum

Author Correction: Pan-cancer deconvolution of tumour composition using DNA methylation

0 references

author

Matt Lechner

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Sergio A Quezada

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Andrew Feber

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Tim R Fenton

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

author name string

Ankur Chakravarthy

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Andrew Furness

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Kroopa Joshi

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Ehsan Ghorani

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Kirsty Ford

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Matthew J Ward

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Emma V King

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Teresa Marafioti

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

Gareth J Thomas

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

language of work or name

English

0 references

publication date

13 August 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

published in

Nature Communications

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

page(s)

3220

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

17 April 2020

copyright license

start time

13 August 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/6089972

based on heuristic

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1038/s41467-018-05570-1

0 references

cites work

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma.

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A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing

2 November 2018

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Epigenetic Therapy Ties MYC Depletion to Reversing Immune Evasion and Treating Lung Cancer.

2 November 2018

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Universal Patterns of Selection in Cancer and Somatic Tissues

2 November 2018

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Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab

2 November 2018

1 reference

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Targeting the Myofibroblastic Cancer-Associated Fibroblast Phenotype Through Inhibition of NOX4.

2 November 2018

1 reference

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Identification of essential genes for cancer immunotherapy.

2 November 2018

1 reference

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The immune contexture in cancer prognosis and treatment

2 November 2018

1 reference

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Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance.

2 November 2018

1 reference

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Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma.

2 November 2018

1 reference

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Human Tumor-Infiltrating Myeloid Cells: Phenotypic and Functional Diversity

2 November 2018

1 reference

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A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

2 November 2018

1 reference

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Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.

2 November 2018

1 reference

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Human Papillomavirus Drives Tumor Development Throughout the Head and Neck: Improved Prognosis Is Associated With an Immune Response Largely Restricted to the Oropharynx.

2 November 2018

1 reference

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Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.

2 November 2018

1 reference

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Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

2 November 2018

1 reference

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Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

A landscape of pharmacogenomic interactions in cancer.

2 November 2018

1 reference

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Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Landscape of tumor-infiltrating T cell repertoire of human cancers

2 November 2018

1 reference

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Upregulated Glucose Metabolism Correlates Inversely with CD8+ T-cell Infiltration and Survival in Squamous Cell Carcinoma.

2 November 2018

1 reference

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Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Near-optimal probabilistic RNA-seq quantification

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Tumor infiltrating lymphocytes and survival in patients with head and neck squamous cell carcinoma

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

EGFR Signaling Enhances Aerobic Glycolysis in Triple-Negative Breast Cancer Cells to Promote Tumor Growth and Immune Escape

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Systematic pan-cancer analysis of tumour purity

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

De novo transcriptome profiling of highly purified human lymphocytes primary cells

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

The prognostic landscape of genes and infiltrating immune cells across human cancers

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Robust enumeration of cell subsets from tissue expression profiles

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

2 November 2018

1 reference

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PD-L1 Expression as a Predictive Biomarker in Cancer Immunotherapy

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Comprehensive genomic characterization of head and neck squamous cell carcinomas

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Functional normalization of 450k methylation array data improves replication in large cancer studies.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Molecular and genetic properties of tumors associated with local immune cytolytic activity

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Integrative analysis of head and neck cancer identifies two biologically distinct HPV and three non-HPV subtypes

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Expanding epigenomics to archived FFPE tissues: an evaluation of DNA repair methodologies

2 November 2018

1 reference

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Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Impact of tumour microenvironment and Fc receptors on the activity of immunomodulatory antibodies

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Caspase-8 mutations in head and neck cancer confer resistance to death receptor-mediated apoptosis and enhance migration, invasion, and tumor growth

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Staging and treatment of oropharyngeal cancer in the human papillomavirus era.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

2 November 2018

1 reference

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Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Reference-free cell mixture adjustments in analysis of DNA methylation data

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Discovery and saturation analysis of cancer genes across 21 tumour types

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Tumour-infiltrating lymphocytes predict for outcome in HPV-positive oropharyngeal cancer.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Tumour-infiltrating lymphocytes predict response to definitive chemoradiotherapy in head and neck cancer.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Inferring tumour purity and stromal and immune cell admixture from expression data

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

From the immune contexture to the Immunoscore: the role of prognostic and predictive immune markers in cancer

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Absolute quantification of somatic DNA alterations in human cancer

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

The prognostic value of FoxP3+ tumor-infiltrating lymphocytes in cancer: a critical review of the literature

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Human papillomavirus predicts outcome in oropharyngeal cancer in patients treated primarily with surgery or radiation therapy

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Is the improved prognosis of p16 positive oropharyngeal squamous cell carcinoma dependent of the treatment modality?

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Intraepithelial CD8+ tumor-infiltrating lymphocytes and a high CD8+/regulatory T cell ratio are associated with favorable prognosis in ovarian cancer

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6089972

Stromal features are predictive of disease mortality in oral cancer patients

2 November 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-018-05570-1

inferred from DOI database lookup

7 January 2021

based on heuristic

Intratumoral CD8(+) T/FOXP3 (+) cell ratio is a predictive marker for survival in patients with colorectal cancer

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-018-05570-1

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/S41467-018-05570-1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30104673%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

1 reference