(Q36040381)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

title

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Lynn Bry

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

author name string

Belinda Tzen

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Ning Li

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Matt Simmons

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Takeshi Tanoue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Elijah Bogart

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Luxue Deng

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Vladimir Yeliseyev

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Mary L Delaney

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Qing Liu

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Bernat Olle

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Richard R Stein

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Kenya Honda

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Georg K Gerber

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

publication date

3 June 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

volume

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

page(s)

121

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

3 April 2020

DESeq2

object named as

DESeq2

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/s13059-016-0980-6

0 references

cites work

Biogeography of a human oral microbiome at the micron scale

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Gut biogeography of the bacterial microbiota

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Reciprocal interaction of diet and microbiome in inflammatory bowel diseases.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

HUMAN MICROBIOTA. Small molecules from the human microbiota

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Diet dominates host genotype in shaping the murine gut microbiota

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Dynamics of the microbiota in response to host infection

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Towards predictive models of the human gut microbiome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Waste not, want not: why rarefying microbiome data is inadmissible

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

2 October 2017

The dynamic microbiome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Mathematical modeling of primary succession of murine intestinal microbiota.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Diet and inflammatory bowel disease: review of patient-targeted recommendations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

nhmmer: DNA homology search with profile HMMs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Xenobiotics shape the physiology and gene expression of the active human gut microbiome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Duodenal infusion of donor feces for recurrent Clostridium difficile

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Hypothesis testing and power calculations for taxonomic-based human microbiome data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Inferring correlation networks from genomic survey data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Detecting causality in complex ecosystems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Inferring dynamic signatures of microbes in complex host ecosystems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

The gusBC genes of Escherichia coli encode a glucuronide transport system

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Lactobacillus reuteri CRL1098 produces cobalamin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

An in vitro study of the probiotic potential of a bile-salt-hydrolyzing Lactobacillus fermentum strain, and determination of its cholesterol-lowering properties

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menA gene from Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Formation of ursodeoxycholic acid from chenodeoxycholic acid by a 7 beta-hydroxysteroid dehydrogenase-elaborating Eubacterium aerofaciens strain cocultured with 7 alpha-hydroxysteroid dehydrogenase-elaborating organisms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Biosynthesis of vitamin K (menaquinone) in bacteria

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Deconjugation of bile acids by intestinal lactobacilli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

An ecological network of polysaccharide utilization among human intestinal symbionts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Production of vitamin B 12 analogues in patients with small-bowel bacterial overgrowth

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Fermentations by saccharolytic intestinal bacteria

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Distribution of beta-glucosidase and beta-glucuronidase activity and of beta-glucuronidase gene gus in human colonic bacteria.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

Degradation of bile salts by human intestinal bacteria

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4893271

23 September 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0980-6

7alpha-dehydroxylation of cholic acid by Clostridium bifermentans strain ATCC 9714 and Clostridium sordellii strain NCIB 6929

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27259475

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Regression Models For Multivariate Count Data

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27259475

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Separation of 7 alpha- and 7 beta-hydroxysteroid dehydrogenase activities from clostridium absonum ATCC# 27555 and cellular response of this organism to bile acid inducers

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27259475

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-016-0980-6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

3 April 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27259475%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

PubMed publication ID

27259475

1 reference