Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Community structure follows simple assembly rules in microbial microcosms

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

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

(2016) Toshitaka Odamaki et al.   BMC MICROBIOLOGY

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Oscillospira : a Central, Enigmatic Component of the Human Gut Microbiota

(2016) Tom Konikoff et al.   TRENDS IN MICROBIOLOGY

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

(2016) Marc A. Sze et al.   mBio

Signatures of early frailty in the gut microbiota

(2016) Matthew A. Jackson et al.   Genome Medicine

A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

(2016) Matthew A. Jackson et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease

(2016) Steven N. Baldassano et al.   Scientific Reports

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia

(2014) Marius Vital et al.   ISME Journal

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

(2013) Karen De Roy et al.   ENVIRONMENTAL MICROBIOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease

(2013) Maomeng Tong et al.   PLoS One

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Significant Scales in Community Structure

(2013) V. A. Traag et al.   Scientific Reports

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

(2013) Ian H McHardy et al.   Microbiome

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

(2012) C. Lozupone et al.   GENOME RESEARCH

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

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

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Correlation Network Analysis Applied to Complex Biofilm Communities

(2011) Ana E. Duran-Pinedo et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Diet, gut microbiota and immune responses

(2010) Kendle M Maslowski et al.   NATURE IMMUNOLOGY

Community Structure in Time-Dependent, Multiscale, and Multiplex Networks

(2010) P. J. Mucha et al.   SCIENCE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice

(2009) Z. Gao et al.   DIABETES

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Multiresolution community detection for megascale networks by information-based replica correlations

(2009) Peter Ronhovde et al.   PHYSICAL REVIEW E

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA