Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

(2017) Alex D. Washburne et al.   PeerJ

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Persisting changes of intestinal microbiota after bowel lavage and colonoscopy

(2016) Lorenzo Drago et al.   EUROPEAN JOURNAL OF GASTROENTEROLOGY & HEPATOLOGY

A guide through a family of phylogenetic dissimilarity measures among sites

(2016) Sandrine Pavoine   OIKOS

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Impact of demographics on human gut microbial diversity in a US Midwest population

(2016) Jun Chen et al.   PeerJ

The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments

(2016) Rima M Shobar et al.   Clinical and Translational Gastroenterology

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

(2016) Euan Watt et al.   Microbiome

The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects

(2015) I. Rangel et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

The microbiome in asthma

(2015) Yvonne J. Huang et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Global, regional, and national age–sex specific all-cause and cause-specific mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

(2015)   LANCET

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans

(2015) Lawrence A. David et al.   mBio

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data

(2015) Kris Sankaran et al.   Journal of Statistical Software

The human microbiome and bile acid metabolism: dysbiosis, dysmetabolism, disease and intervention

(2014) Mitchell L Jones et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Effects of bowel cleansing on the intestinal microbiota

(2014) Jonna Jalanka et al.   GUT

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

(2014) Anne Salonen et al.   ISME Journal

Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)

(2014) S. Dray et al.   Molecular Ecology Resources

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Links between diet, gut microbiota composition and gut metabolism

(2014) Harry J. Flint et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

Gut Microbiome Perturbations Induced by Bacterial Infection Affect Arsenic Biotransformation

(2013) Kun Lu et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria,in vitro

(2013) Karen P. Scott et al.   FEMS MICROBIOLOGY ECOLOGY

A refined palate: Bacterial consumption of host glycans in the gut

(2013) A. Marcobal et al.   GLYCOBIOLOGY

A decrease of the butyrate-producing speciesRoseburia hominisandFaecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis

(2013) Kathleen Machiels et al.   GUT

Intestinal Microbial Metabolism of Phosphatidylcholine and Cardiovascular Risk

(2013) W.H. Wilson Tang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea

(2013) Gregor Gorkiewicz et al.   PLoS One

Impact of Colonoscopy Bowel Preparation on Intestinal Microbiota

(2013) Claire L. O’Brien et al.   PLoS One

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

(2012) Jean Guy LeBlanc et al.   CURRENT OPINION IN BIOTECHNOLOGY

Long-term monitoring of the human intestinal microbiota composition

(2012) Mirjana Rajilić-Stojanović et al.   ENVIRONMENTAL MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

IBD—what role do Proteobacteria play?

(2012) Indrani Mukhopadhya et al.   Nature Reviews Gastroenterology & Hepatology

Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance

(2012) Robert A. Britton et al.   TRENDS IN MICROBIOLOGY

Analysis of a data matrix and a graph: Metagenomic data and the phylogenetic tree

(2011) Elizabeth Purdom   Annals of Applied Statistics

Metabolomics of Fecal Extracts Detects Altered Metabolic Activity of Gut Microbiota in Ulcerative Colitis and Irritable Bowel Syndrome

(2011) Gwénaëlle Le Gall et al.   JOURNAL OF PROTEOME RESEARCH

Evidence of cellulose metabolism by the giant panda gut microbiome

(2011) L. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Fecal Microbiota in Infants with and without Eczema

(2010) Pei-Ying Hong et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

(2008) Alan W. Walker et al.   ENVIRONMENTAL MICROBIOLOGY

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

(2008) Li Wen et al.   NATURE