An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Signatures of ecological processes in microbial community time series

(2018) Karoline Faust et al.   Microbiome

Microbiome interactions shape host fitness

(2018) Alison L. Gould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts

(2018) Justin D. Silverman et al.   Microbiome

Modeling time-series data from microbial communities

(2017) Benjamin J Ridenhour et al.   ISME Journal

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice

(2017) Eveliina Munukka et al.   ISME Journal

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals

(2017) M. Andrea Azcarate-Peril et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

The Gut Microbiota and Autism Spectrum Disorders

(2017) Qinrui Li et al.   Frontiers in Cellular Neuroscience

Two dynamic regimes in the human gut microbiome

(2017) Sean M. Gibbons et al.   PLoS Computational Biology

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels

(2017) Tiantian Ren et al.   Microbiome

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Community structure follows simple assembly rules in microbial microcosms

(2017) Jonathan Friedman et al.   Nature Ecology & Evolution

Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons

(2016) Hong-Tai Cao et al.   BIOESSAYS

@MInter: automated text-mining of microbial interactions

(2016) Kun Ming Kenneth Lim et al.   BIOINFORMATICS

Microbial interactions and community assembly at microscales

(2016) Otto X Cordero et al.   CURRENT OPINION IN MICROBIOLOGY

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes

(2016) Chenhong Zhang et al.   ISME Journal

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Laboratory Evolution of Microbial Interactions in Bacterial Biofilms

(2016) Marivic Martin et al.   JOURNAL OF BACTERIOLOGY

Predicting microbial interactions through computational approaches

(2016) Chenhao Li et al.   METHODS

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Bacterial predator–prey dynamics in microscale patchy landscapes

(2016) Felix J. H. Hol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Measuring the biodiversity of microbial communities by flow cytometry

(2016) Ruben Props et al.   Methods in Ecology and Evolution

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare

(2016) Kern Rei Chng et al.   Nature Microbiology

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Fate, activity, and impact of ingested bacteria within the human gut microbiota

(2015) Muriel Derrien et al.   TRENDS IN MICROBIOLOGY

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Bacteria–bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance

(2014) Sebastian Fraune et al.   ISME Journal

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

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

(2014) Marc A. Sze et al.   PLoS One

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Mathematical modeling of primary succession of murine intestinal microbiota

(2013) S. Marino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Unbalance of intestinal microbiota in atopic children

(2012) Marco Candela et al.   BMC MICROBIOLOGY

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Bacteroides uniformis CECT 7771 Ameliorates Metabolic and Immunological Dysfunction in Mice with High-Fat-Diet Induced Obesity

(2012) Paola Gauffin Cano et al.   PLoS One

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Mathematical modeling of gene expression: a guide for the perplexed biologist

(2011) Ahmet Ay et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Bacteria and host interactions in the gut epithelial barrier

(2011) Hiroshi Ashida et al.   Nature Chemical Biology

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Soil beneficial bacteria and their role in plant growth promotion: a review

(2010) Rifat Hayat et al.   ANNALS OF MICROBIOLOGY

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

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Digital PCR provides sensitive and absolute calibration for high throughput sequencing

(2009) Richard A White et al.   BMC GENOMICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

What is the expectation maximization algorithm?

(2008) Chuong B Do et al.   NATURE BIOTECHNOLOGY