Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota

Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors

(2019) Shirin Moossavi et al.   Cell Host & Microbe

Rigorous Statistical Methods for Rigorous Microbiome Science

(2019) Amy D. Willis   mSystems

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination

(2019) Josef Dahlberg et al.   PLoS One

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

(2019) Lisa Karstens et al.   mSystems

Interrogating the microbiome: experimental and computational considerations in support of study reproducibility

(2018) Carine Poussin et al.   DRUG DISCOVERY TODAY

Correcting for batch effects in case-control microbiome studies

(2018) Sean M. Gibbons et al.   PLoS Computational Biology

Recognizing the reagent microbiome

(2018) Marcus C. de Goffau et al.   Nature Microbiology

Batch effects correction for microbiome data with Dirichlet-multinomial regression

(2018) Zhenwei Dai et al.   BIOINFORMATICS

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

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

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

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

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

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms

(2015) Hooman Derakhshani et al.   JOURNAL OF BASIC MICROBIOLOGY

The Canadian Healthy Infant Longitudinal Development (CHILD) Study: examining developmental origins of allergy and asthma: Table 1

(2015) Padmaja Subbarao et al.   THORAX

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

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

(2012) J Gregory Caporaso et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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