(Q54939975)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

title

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

0 references

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Francesco Rubino

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Christopher J. Creevey

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

5

Karen Siu-Ting

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

author name string

Maximillian Friedersdorff

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Toby J Wilkinson

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Sharon A Huws

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Joan E Edwards

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Alison H Kingston-Smith

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

publication date

25 May 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

Frontiers in Microbiology

30 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

page(s)

1095

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

30 March 2020

copyright license

start time

25 May 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

ggplot2

object named as

ggplot2

2 references

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5981159

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

DESeq2

object named as

DESeq2

1 reference

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

cites work

Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet

1 reference

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A genomic perspective on stoichiometric regulation of soil carbon cycling

14 June 2018

1 reference

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Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys.

14 June 2018

1 reference

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The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

14 June 2018

1 reference

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Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

An Integrated Multi-Omics Approach Reveals the Effects of Supplementing Grass or Grass Hay with Vitamin E on the Rumen Microbiome and Its Function

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Development of Ruminal and Fecal Microbiomes Are Affected by Weaning But Not Weaning Strategy in Dairy Calves

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Manipulating rumen microbiome and fermentation through interventions during early life: a review

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

The vocabulary of microbiome research: a proposal

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Rumen microbiome from steers differing in feed efficiency

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

STAMP: statistical analysis of taxonomic and functional profiles.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Determining the culturability of the rumen bacterial microbiome

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Prokka: rapid prokaryotic genome annotation

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

clusterProfiler: an R package for comparing biological themes among gene clusters.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Advances in microbial ecosystem concepts and their consequences for ruminant agriculture.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Fast gapped-read alignment with Bowtie 2

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Mutualistic fermentative digestion in the gastrointestinal tract: diversity and evolution

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

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

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Search and clustering orders of magnitude faster than BLAST

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

QIIME allows analysis of high-throughput community sequencing data

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

KEGG: kyoto encyclopedia of genes and genomes

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Why prokaryotes have pangenomes

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

The khmer software package: enabling efficient nucleotide sequence analysis

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

Plant-based strategies towards minimising 'livestock's long shadow'.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5981159

13 August 2018

Identifiers

DOI

10.3389/FMICB.2018.01095

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29887853%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference