Related references
Note: Only part of the references are listed.Deciphering microbial interactions in synthetic human gut microbiome communities
Ophelia S. Venturelli et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Signatures of ecological processes in microbial community time series
Karoline Faust et al.
MICROBIOME (2018)
Microbiome interactions shape host fitness
Alison L. Gould et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
Justin D. Silverman et al.
MICROBIOME (2018)
Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons
Hong-Tai Cao et al.
BIOESSAYS (2017)
Absolute quantification of microbial taxon abundances
Ruben Props et al.
ISME JOURNAL (2017)
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Stefania Magnusdottir et al.
NATURE BIOTECHNOLOGY (2017)
Modeling time-series data from microbial communities
Benjamin J. Ridenhour et al.
ISME JOURNAL (2017)
Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice
Eveliina Munukka et al.
ISME JOURNAL (2017)
Quantitative microbiome profiling links gut community variation to microbial load
Doris Vandeputte et al.
NATURE (2017)
Shotgun metagenomics, from sampling to analysis
Christopher Quince et al.
NATURE BIOTECHNOLOGY (2017)
Accessible, curated metagenomic data through ExperimentHub
Edoardo Pasolli et al.
NATURE METHODS (2017)
Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals
M. Andrea Azcarate-Peril et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Samuel A. Smits et al.
SCIENCE (2017)
The Gut Microbiota and Autism Spectrum Disorders
Qinrui Li et al.
FRONTIERS IN CELLULAR NEUROSCIENCE (2017)
Two dynamic regimes in the human gut microbiome
Sean M. Gibbons et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels
Tiantian Ren et al.
MICROBIOME (2017)
Dynamics of the human gut microbiome in inflammatory bowel disease
Jonas Halfvarson et al.
NATURE MICROBIOLOGY (2017)
Community structure follows simple assembly rules in microbial microcosms
Jonathan Friedman et al.
NATURE ECOLOGY & EVOLUTION (2017)
@Minter: automated text-mining of microbial interactions
Kun Ming Kenneth Lim et al.
BIOINFORMATICS (2016)
Microbial interactions and community assembly at microscales
Otto X. Cordero et al.
CURRENT OPINION IN MICROBIOLOGY (2016)
Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes
Chenhong Zhang et al.
ISME JOURNAL (2016)
Laboratory Evolution of Microbial Interactions in Bacterial Biofilms
Marivic Martin et al.
JOURNAL OF BACTERIOLOGY (2016)
Predicting microbial interactions through computational approaches
Chenhao Li et al.
METHODS (2016)
Bacterial predator-prey dynamics in microscale patchy landscapes
Felix J. H. Hol et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2016)
Measuring the biodiversity of microbial communities by flow cytometry
Ruben Props et al.
METHODS IN ECOLOGY AND EVOLUTION (2016)
Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation
Matthew T. Agler et al.
PLOS BIOLOGY (2016)
Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare
Kern Rei Chng et al.
NATURE MICROBIOLOGY (2016)
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
Vanni Bucci et al.
GENOME BIOLOGY (2016)
Networks of energetic and metabolic interactions define dynamics in microbial communities
Mallory Embree et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Structure and function of the global ocean microbiome
Shinichi Sunagawa et al.
SCIENCE (2015)
The ecology of the microbiome: Networks, competition, and stability
Katharine Z. Coyte et al.
SCIENCE (2015)
Fate, activity, and impact of ingested bacteria within the human gut microbiota
Muriel Derrien et al.
TRENDS IN MICROBIOLOGY (2015)
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Zachary D. Kurtz et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Bacteria-bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance
Sebastian Fraune et al.
ISME JOURNAL (2015)
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
Charlie G. Buffie et al.
NATURE (2015)
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
Steven F. Stoddard et al.
NUCLEIC ACIDS RESEARCH (2015)
The Earth Microbiome project: successes and aspirations
Jack A. Gilbert et al.
BMC BIOLOGY (2014)
Alterations of the human gut microbiome in liver cirrhosis
Nan Qin et al.
NATURE (2014)
Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression
Charles K. Fisher et al.
PLOS ONE (2014)
A Comparison between Droplet Digital and Quantitative PCR in the Analysis of Bacterial 16S Load in Lung Tissue Samples from Control and COPD GOLD 2
Marc A. Sze et al.
PLOS ONE (2014)
Mathematical modeling of primary succession of murine intestinal microbiota
Simeone Marino et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Deciphering microbial interactions and detecting keystone species with co-occurrence networks
David Berry et al.
FRONTIERS IN MICROBIOLOGY (2014)
Host lifestyle affects human microbiota on daily timescales
Lawrence A. David et al.
GENOME BIOLOGY (2014)
Differential abundance analysis for microbial marker-gene surveys
Joseph N. Paulson et al.
NATURE METHODS (2013)
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
Richard R. Stein et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Unbalance of intestinal microbiota in atopic children
Marco Candela et al.
BMC MICROBIOLOGY (2012)
The Impact of the Gut Microbiota on Human Health: An Integrative View
Jose C. Clemente et al.
CELL (2012)
Bacteria and host interactions in the gut epithelial barrier
Hiroshi Ashida et al.
NATURE CHEMICAL BIOLOGY (2012)
Bacteroides uniformis CECT 7771 Ameliorates Metabolic and Immunological Dysfunction in Mice with High-Fat-Diet Induced Obesity
Paola Gauffin Cano et al.
PLOS ONE (2012)
Microbial Co-occurrence Relationships in the Human Microbiome
Karoline Faust et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Inferring Correlation Networks from Genomic Survey Data
Jonathan Friedman et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Mathematical modeling of gene expression: a guide for the perplexed biologist
Ahmet Ay et al.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2011)
Competitive and cooperative metabolic interactions in bacterial communities
Shiri Freilich et al.
NATURE COMMUNICATIONS (2011)
Moving pictures of the human microbiome
J. Gregory Caporaso et al.
GENOME BIOLOGY (2011)
Soil beneficial bacteria and their role in plant growth promotion: a review
Rifat Hayat et al.
ANNALS OF MICROBIOLOGY (2010)
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
Carlotta De Filippo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
A scaling normalization method for differential expression analysis of RNA-seq data
Mark D. Robinson et al.
GENOME BIOLOGY (2010)
Digital PCR provides sensitive and absolute calibration for high throughput sequencing
Richard A. White et al.
BMC GENOMICS (2009)
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
John C. Marioni et al.
GENOME RESEARCH (2008)
What is the expectation maximization algorithm?
Chuong B. Do et al.
NATURE BIOTECHNOLOGY (2008)
Microbial interactions within a cheese microbial community
Jerome Mounier et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)
The Human Microbiome Project
Peter J. Turnbaugh et al.
NATURE (2007)
Bacteroides: the good, the bad, and the nitty-gritty
Hannah M. Wexler
CLINICAL MICROBIOLOGY REVIEWS (2007)
Evaluation of quantitative polymerase chain reaction-based approaches for determining gene copy and gene transcript numbers in environmental samples
CJ Smith et al.
ENVIRONMENTAL MICROBIOLOGY (2006)
Quantifying the roles of immigration and chance in shaping prokaryote community structure
WT Sloan et al.
ENVIRONMENTAL MICROBIOLOGY (2006)
Temporal stability and biodiversity of two complex antilisterial cheese-ripening microbial consortia
A Maoz et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)
Quorum sensing in bacteria
MB Miller et al.
ANNUAL REVIEW OF MICROBIOLOGY (2001)
Share Paper
