Correcting for batch effects in case-control microbiome studies

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

(2017) Francislon S Oliveira et al.   NUCLEIC ACIDS RESEARCH

Why Batch Effects Matter in Omics Data, and How to Avoid Them

(2017) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

(2016) Nielson T. Baxter et al.   Genome Medicine

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Geography and Location Are the Primary Drivers of Office Microbiome Composition

(2016) John Chase et al.   mSystems

The Built Environment Is a Microbial Wasteland

(2016) Sean M. Gibbons   mSystems

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

(2016) Emily Vogtmann et al.   PLoS One

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

16S gut community of the Cameron County Hispanic Cohort

(2015) Matthew C Ross et al.   Microbiome

The gut microbiota of Colombians differs from that of Americans, Europeans and Asians

(2014) Juan S Escobar et al.   BMC MICROBIOLOGY

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer

(2014) J. P. Zackular et al.   Cancer Prevention Research

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

Meta-analyses of human gut microbes associated with obesity and IBD

(2014) William A. Walters et al.   FEBS LETTERS

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Parsing ecological signal from noise in next generation amplicon sequencing

(2014) Nhu H. Nguyen et al.   NEW PHYTOLOGIST

Microbiome Data Distinguish Patients with Clostridium difficile Infection and Non-C. difficile-Associated Diarrhea from Healthy Controls

(2014) A. M. Schubert et al.   mBio

Alterations in the Gut Microbiota Associated with HIV-1 Infection

(2013) Catherine A. Lozupone et al.   Cell Host & Microbe

Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome

(2013) Lukasz Krych et al.   PLoS One

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

Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection

(2013) Caroline Vincent et al.   Microbiome

A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects

(2012) Harold Tjalsma et al.   NATURE REVIEWS MICROBIOLOGY

Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

(2012) Weiguang Chen et al.   PLoS One

Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease

(2012) Eliseo Papa et al.   PLoS One

Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome

(2012) Margaret L. Zupancic et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans

(2011) Reiner Jumpertz et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

(2011) Tingting Wang et al.   ISME Journal

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods

(2011) Chao Chen et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics