Metagenomic biomarker discovery and explanation (Q35557728)

8 August 2017

title

Metagenomic biomarker discovery and explanation (English)

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8 August 2017

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8 August 2017

Jacques Izard

2

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Levi Waldron

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Levi Waldron

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3

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Curtis Huttenhower

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Curtis Huttenhower

series ordinal

7

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Dirk Gevers

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4

object named as

Dirk Gevers

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8 August 2017

6

Wendy S Garrett

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8 August 2017

Larisa Miropolsky

5

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8 August 2017

publication date

24 June 2011

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8 August 2017

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8 August 2017

volume

12

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8 August 2017

issue

6

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8 August 2017

page(s)

R60

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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

8 August 2017

cites work

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12 July 2018

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Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes

12 July 2018

1 reference

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Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis

12 July 2018

1 reference

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METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.

12 July 2018

1 reference

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

12 July 2018

1 reference

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Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

12 July 2018

1 reference

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Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

12 July 2018

1 reference

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Metagenomics: Facts and Artifacts, and Computational Challenges*

12 July 2018

1 reference

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Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

12 July 2018

1 reference

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The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice

12 July 2018

1 reference

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Exploring the within- and between-class correlation distributions for tumor classification

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Environmental distribution of prokaryotic taxa

12 July 2018

1 reference

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12 July 2018

A primer on metagenomics

1 reference

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Incorporating prior knowledge to facilitate discoveries in a genome-wide association study on age-related macular degeneration

12 July 2018

1 reference

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Identifying biologically relevant differences between metagenomic communities

12 July 2018

1 reference

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Galaxy: a web-based genome analysis tool for experimentalists

12 July 2018

1 reference

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Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

A high-throughput DNA sequence aligner for microbial ecology studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Salivary transcriptomic biomarkers for detection of resectable pancreatic cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Probiotics and gastrointestinal disease: successes, problems and future prospects

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Inclusion of a priori information in genome-wide association analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Bacterial community variation in human body habitats across space and time

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The clinical value of salivary biomarkers for periodontal disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Intestinal mucosal barrier function in health and disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The NIH Human Microbiome Project

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Using prior knowledge and genome-wide association to identify pathways involved in multiple sclerosis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Statistical methods for detecting differentially abundant features in clinical metagenomic samples

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Biomarkers for infants at risk for necrotizing enterocolitis: clues to prevention?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Exploring the diversity of the bifidobacterial population in the human intestinal tract

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

A core gut microbiome in obese and lean twins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Human colonic microbiota associated with diet, obesity and weight loss

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Substantial alterations of the cutaneous bacterial biota in psoriatic lesions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Functional metagenomic profiling of nine biomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

An ecological and evolutionary perspective on human-microbe mutualism and disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The human microbiome project

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Metascardovia criceti Gen. Nov., Sp. Nov., from hamster dental plaque

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Accuracy and quality of massively parallel DNA pyrosequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

MEGAN analysis of metagenomic data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

An obesity-associated gut microbiome with increased capacity for energy harvest

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Microbial diversity in the deep sea and the underexplored "rare biosphere"

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Mechanisms of Disease: pathogenesis of Crohn's disease and ulcerative colitis

12 July 2018

1 reference

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Marine microbial diversity: can it be determined?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Metagenomics: the role of the microbiome in cardiovascular diseases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Ecological and evolutionary forces shaping microbial diversity in the human intestine

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

UniFrac: a new phylogenetic method for comparing microbial communities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Comparative metagenomics of microbial communities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Host specificity in marine sponge-associated bacteria, and potential implications for marine microbial diversity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Treatment of ulcerative colitis using fecal bacteriotherapy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Mouse models for the study of Crohn's disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

High-throughput gene mapping in Caenorhabditis elegans

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Use of proteomic patterns in serum to identify ovarian cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Significance analysis of microarrays applied to the ionizing radiation response

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The COG database: new developments in phylogenetic classification of proteins from complete genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Development of colonic adenocarcinomas in a mouse model of ulcerative colitis.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

A genomic perspective on protein families

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Identification of the uncultured bacillus of Whipple's disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Survival of Campylobacter jejuni under conditions of atmospheric oxygen tension with the support of Pseudomonas spp.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Comparison of multiple metagenomes using phylogenetic networks based on ecological indices

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Over-optimism in bioinformatics research

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Visual and statistical comparison of metagenomes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Low counts of Faecalibacterium prausnitzii in colitis microbiota.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Oral cavity as natural reservoir for intestinal lactobacilli.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

False discovery rate, sensitivity and sample size for microarray studies.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Rarity associated with specific ecological niches in the bacterial world: the 'Synergistes' example

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

A novel model of inflammatory bowel disease: mice deficient for the multiple drug resistance gene, mdr1a, spontaneously develop colitis.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

The 'rare biosphere': a reality check

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3218848

Maladie immunoproliférative de l'intestin grêle associée à Campylobacter jejuni

15 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21702898

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mouse models of inflammatory bowel disease

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21702898

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Successful treatment of fulminant Clostridium difficile infection with fecal bacteriotherapy

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21702898

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GB-2011-12-6-R60

1 reference

Dimensions Publication ID

8 August 2017

0 references

1 reference

8 August 2017

1 reference