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

clValid: AnRPackage for Cluster Validation

(2015) Guy Brock et al.   Journal of Statistical Software

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

A systematic comparison of genome-scale clustering algorithms

(2012) Jeremy J Jay 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

Host genes related to Paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition

(2012) Tianyi Zhang et al.   INFLAMMATORY BOWEL DISEASES

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition

(2012) Ellen Li et al.   PLoS One

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Metagenomics and Personalized Medicine

(2011) Herbert W. Virgin et al.   CELL

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

(2011) M. Joossens et al.   GUT

Role of the microbiota in inflammatory bowel diseases

(2011) Nabeetha A. Nagalingam et al.   INFLAMMATORY BOWEL DISEASES

Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California

(2011) J Michael Beman et al.   ISME Journal

Loss of intestinal core 1–derived O-glycans causes spontaneous colitis in mice

(2011) Jianxin Fu et al.   JOURNAL OF CLINICAL INVESTIGATION

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Intestinal homeostasis and its breakdown in inflammatory bowel disease

(2011) Kevin J. Maloy et al.   NATURE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Erratum: Corrigendum: Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

(2011) Carl A Anderson et al.   NATURE GENETICS

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface

(2011) Xiaoxiao Li et al.   PLoS One

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

(2011) P. Rausch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Investigating the biological and clinical significance of human dysbioses

(2011) Daniel N. Frank et al.   TRENDS IN MICROBIOLOGY

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

(2011) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Recent advances in clustering methods for protein interaction networks

(2010) Jianxin Wang et al.   BMC GENOMICS

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

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

(2010) S. Chaffron et al.   GENOME RESEARCH

Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases

(2010) Daniel N. Frank et al.   INFLAMMATORY BOWEL DISEASES

Characterization of Escherichia coli isolated from gut biopsies of newly diagnosed patients with inflammatory bowel disease

(2010) Shadi Sepehri et al.   INFLAMMATORY BOWEL DISEASES

From Structure to Function: the Ecology of Host-Associated Microbial Communities

(2010) C. J. Robinson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

(2010) A. K. Benson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria

(2010) Z. M. Summers et al.   SCIENCE

Papers on normalization, variable selection, classification or clustering of microarray data

(2009) D. M. Rocke et al.   BIOINFORMATICS

Mouse models of intestinal inflammation as tools to understand the pathogenesis of inflammatory bowel disease

(2009) Holm H. Uhlig et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

What is microbial community ecology?

(2009) Allan Konopka   ISME Journal

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer

(2008) Raffaele Giancarlo et al.   BMC BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases

(2008) Daniel A. Peterson et al.   Cell Host & Microbe

War and Peace at the Intestinal Epithelial Surface: An Integrated View of Bacterial Commensalism Versus Bacterial Pathogenicity

(2008) &NA;   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Network Relationships of Bacteria in a Stable Mixed Culture

(2008) Souichiro Kato et al.   MICROBIAL ECOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Molecular eco-systems biology: towards an understanding of community function

(2008) Jeroen Raes et al.   NATURE REVIEWS MICROBIOLOGY

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

Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41

(2008) B. S. Samuel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geometric Interpretation of Gene Coexpression Network Analysis

(2008) Steve Horvath et al.   PLoS Computational Biology