Environmental factors shaping the gut microbiome in a Dutch population

Challenges in benchmarking metagenomic profilers

(2021) Zheng Sun et al.   NATURE METHODS

Cigarette smoking status alters dysbiotic gut microbes in hypertensive patients

(2021) Pan Wang et al.   Journal of Clinical Hypertension

Impact of Clostridium Bacteria in Children with Autism Spectrum Disorder and Their Anthropometric Measurements

(2020) Wafaa A. Kandeel et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing

(2020) Farnaz Fouladi et al.   ENVIRONMENT INTERNATIONAL

DeepMicro: deep representation learning for disease prediction based on microbiome data

(2020) Min Oh et al.   Scientific Reports

Impact of air quality on the gastrointestinal microbiome: A review

(2020) Charlotte E. Dujardin et al.   ENVIRONMENTAL RESEARCH

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

(2020) Lianmin Chen et al.   Nature Communications

First microbiome-based drug clears phase III, in clinical trial turnaround

(2020) Ken Garber   NATURE REVIEWS DRUG DISCOVERY

Health and disease markers correlate with gut microbiome composition across thousands of people

(2020) Ohad Manor et al.   Nature Communications

The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1

(2019) Floris Imhann et al.   BMC GASTROENTEROLOGY

Transforming medicine with the microbiome

(2019) Niv Zmora et al.   Science Translational Medicine

Seasonal variation of diet quality in a large middle-aged and elderly Dutch population-based cohort

(2019) Janine E. van der Toorn et al.   EUROPEAN JOURNAL OF NUTRITION

Mapping human microbiome drug metabolism by gut bacteria and their genes

(2019) Michael Zimmermann et al.   NATURE

Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment

(2019) RunYue Huang et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

(2019) Emily R Leeming et al.   Nutrients

lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals

(2018) Andrey Ziyatdinov et al.   BMC BIOINFORMATICS

Development of the food-based Lifelines Diet Score (LLDS) and its application in 129,369 Lifelines participants

(2018) Petra C. Vinke et al.   EUROPEAN JOURNAL OF CLINICAL NUTRITION

Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities

(2018) Dachao Liang et al.   Gut Pathogens

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

The influence of ethnicity and geography on human gut microbiome composition

(2018) Christopher A. Gaulke et al.   NATURE MEDICINE

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

(2018) Tommi Vatanen et al.   Nature Microbiology

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome

(2017) Julien Tap et al.   GASTROENTEROLOGY

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug

(2017) Hao Wu et al.   NATURE MEDICINE

A Protein Diet Score, Including Plant and Animal Protein, Investigating the Association with HbA1c and eGFR—The PREVIEW Project

(2017) Grith Møller et al.   Nutrients

A National Dietary Assessment Reference Database (NDARD) for the Dutch Population: Rationale behind the Design

(2017) Elske Brouwer-Brolsma et al.   Nutrients

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

Association of host genome with intestinal microbial composition in a large healthy cohort

(2016) Williams Turpin et al.   NATURE GENETICS

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

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

(2016) Alexandra Zhernakova et al.   SCIENCE

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

(2016) Hailiang Xie et al.   Cell Systems

Proton pump inhibitors affect the gut microbiome

(2015) Floris Imhann et al.   GUT

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Role of environmental pollution in irritable bowel syndrome

(2015) Mateusz Marynowski   WORLD JOURNAL OF GASTROENTEROLOGY

Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics

(2015) Ettje F Tigchelaar et al.   BMJ Open

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Cohort Profile: LifeLines, a three-generation cohort study and biobank

(2014) Salome Scholtens et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Seasonal Variation in Human Gut Microbiome Composition

(2014) Emily R. Davenport et al.   PLoS One

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

(2014) David Berry et al.   Frontiers in Microbiology

Development of NO2 and NOx land use regression models for estimating air pollution exposure in 36 study areas in Europe – The ESCAPE project

(2013) Rob Beelen et al.   ATMOSPHERIC ENVIRONMENT

Faecalibacterium prausnitzii and human intestinal health

(2013) S Miquel et al.   CURRENT OPINION IN MICROBIOLOGY

Validation of the Rome III Criteria for the Diagnosis of Irritable Bowel Syndrome in Secondary Care

(2013) Alexander C. Ford et al.   GASTROENTEROLOGY

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Development of Land Use Regression Models for PM2.5, PM2.5 Absorbance, PM10 and PMcoarse in 20 European Study Areas; Results of the ESCAPE Project

(2012) Marloes Eeftens et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

(2011) Morris A Swertz et al.   BMC BIOINFORMATICS

Self-reported energy intake by FFQ compared with actual energy intake to maintain body weight in 516 adults

(2011) Els Siebelink et al.   BRITISH JOURNAL OF NUTRITION

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Stability of measured and modelled spatial contrasts in NO2 over time

(2011) M. Eeftens et al.   OCCUPATIONAL AND ENVIRONMENTAL MEDICINE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The rare biosphere: sorting out fact from fiction

(2010) Mitchell L Sogin et al.   GENOME BIOLOGY