(Q55355191)

http://europepmc.org/abstract/PMC/5830445

3 July 2018

title

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. (English)

1 reference

http://europepmc.org/abstract/PMC/5830445

3 July 2018

1 reference

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Mick Watson

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Marc D Auffret

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Maximilian O Press

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Tim J Snelling

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Richard James Dewhurst

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Rainer Roehe

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

author name string

Robert D Stewart

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Amanda Warr

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Andrew H Wiser

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Kyle W Langford

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Ivan Liachko

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

language of work or name

English

0 references

publication date

28 February 2018

1 reference

http://europepmc.org/abstract/PMC/5830445

3 July 2018

published in

Nature Communications

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

page(s)

870

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

5 June 2020

copyright license

start time

28 February 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/s41467-018-03317-6

0 references

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10 July 2018

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10 July 2018

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10 July 2018

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Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs.

10 July 2018

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Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows.

10 July 2018

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Description of two novel members of the family Erysipelotrichaceae: Ileibacteriumvalens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium.

10 July 2018

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10 July 2018

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Centrifuge: rapid and sensitive classification of metagenomic sequences

10 July 2018

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Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

10 July 2018

1 reference

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Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit.

10 July 2018

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Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae.

10 July 2018

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Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids

10 July 2018

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Recovering complete and draft population genomes from metagenome datasets

10 July 2018

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ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

10 July 2018

1 reference

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Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

10 July 2018

1 reference

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Insights into the Role of Erysipelotrichaceae in the Human Host.

10 July 2018

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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

10 July 2018

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The rumen microbial metagenome associated with high methane production in cattle

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Successful test launch for nanopore sequencing

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Prepartum and postpartum rumen fluid microbiomes: characterization and correlation with production traits in dairy cows

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Fast and sensitive protein alignment using DIAMOND

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

10 July 2018

1 reference

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10 July 2018

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Illuminating the future of DNA sequencing

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Trimmomatic: a flexible trimmer for Illumina sequence data

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Kraken: ultrafast metagenomic sequence classification using exact alignments

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Pfam: the protein families database

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

The carbohydrate-active enzymes database (CAZy) in 2013

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

BLAST+: architecture and applications

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

The Sequence Alignment/Map format and SAMtools

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Fast and accurate short read alignment with Burrows-Wheeler transform

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Biopython: freely available Python tools for computational molecular biology and bioinformatics

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Localization of ruminal cellulolytic bacteria on plant fibrous materials as determined by fluorescence in situ hybridization and real-time PCR

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

GenomeDiagram: a python package for the visualization of large-scale genomic data.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Community structure and metabolism through reconstruction of microbial genomes from the environment

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Properties of a fatty acid forming organism isolated from the rumen of sheep

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Phylogenic and phenotypic characterization of some Eubacterium-like isolates from human feces: description of Solobacterium moorei Gen. Nov., Sp. Nov.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Ability of Acidaminococcus fermentans to oxidize trans-aconitate and decrease the accumulation of tricarballylate, a toxic end product of ruminal fermentation

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Emendation of the Description of Acidaminococcus fermentans, a trans-Aconitate- and Citrate-Oxidizing Bacterium

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

The cellulosome--a treasure-trove for biotechnology

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

The characterization of lactic acid producing bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

Improved extraction of PCR-quality community DNA from digesta and fecal samples

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5830445

On the resemblance and containment of documents

12 August 2018

1 reference

https://api.crossref.org/works/10.1038%2FS41467-018-03317-6

7 January 2021

Rumen pH and fermentation characteristics in dairy cows supplemented with Megasphaera elsdenii NCIMB 41125 in early lactation

1 reference

https://api.crossref.org/works/10.1038%2FS41467-018-03317-6

7 January 2021

Regulation of fermentation in a ruminal bacterium, Streptococcus bovis, with special reference to rumen acidosis

1 reference

https://api.crossref.org/works/10.1038%2FS41467-018-03317-6

7 January 2021

Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens

1 reference

https://api.crossref.org/works/10.1038%2FS41467-018-03317-6

7 January 2021

Corrigendum: Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacter

1 reference

https://api.crossref.org/works/10.1038%2FS41467-018-03317-6

7 January 2021

10.1038/S41467-018-03317-6

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

5 June 2020

ADS bibcode

2018NatCo...9..870S

0 references

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29491419%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

1 reference