Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research

Robust research needs many lines of evidence

(2018) Marcus R. Munafò et al.   NATURE

An empirical analysis of journal policy effectiveness for computational reproducibility

(2018) Victoria Stodden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The importance of being second

(2018)   PLOS BIOLOGY

“Available upon request”: not good enough for microbiome data!

(2018) Morgan G. I. Langille et al.   Microbiome

Good enough practices in scientific computing

(2017) Greg Wilson et al.   PLoS Computational Biology

Ten simple rules for making research software more robust

(2017) Morgan Taschuk et al.   PLoS Computational Biology

Optimizing methods and dodging pitfalls in microbiome research

(2017) Dorothy Kim et al.   Microbiome

A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

(2017) Maria Elisa Perez-Muñoz et al.   Microbiome

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment

(2017) Katy J. Califf et al.   mSystems

Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes

(2017) Matthew L. Jenior et al.   mSystems

Investigation of Cross-Contamination and Misidentification of 278 Widely Used Tumor Cell Lines

(2017) Yaqing Huang et al.   PLoS One

The ghosts of HeLa: How cell line misidentification contaminates the scientific literature

(2017) Serge P. J. M. Horbach et al.   PLoS One

Genetic Determinants of the Gut Microbiome in UK Twins

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

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

(2016) Alexandra Zhernakova et al.   SCIENCE

What does research reproducibility mean?

(2016) Steven N. Goodman et al.   Science Translational Medicine

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

(2016) Marc A. Sze et al.   mBio

A Framework for Improving the Quality of Research in the Biological Sciences

(2016) Arturo Casadevall et al.   mBio

Ten Simple Rules for Digital Data Storage

(2016) Edmund M. Hart et al.   PLoS Computational Biology

Ten Simple Rules for Taking Advantage of Git and GitHub

(2016) Yasset Perez-Riverol et al.   PLoS Computational Biology

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

A Bayesian Perspective on the Reproducibility Project: Psychology

(2016) Alexander Etz et al.   PLoS One

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

The unseen world: reflections on Leeuwenhoek (1677) 'Concerning little animals'

(2015) N. Lane   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Opinion: Reproducible research can still be wrong: Adopting a prevention approach: Fig. 1.

(2015) Jeffrey T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

After the bombs

(2015) E. Pain   SCIENCE

The Extent and Consequences of P-Hacking in Science

(2015) Megan L. Head et al.   PLOS BIOLOGY

The Statistical Crisis in Science

(2014) Andrew Gelman et al.   AMERICAN SCIENTIST

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

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

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

Policy: NIH plans to enhance reproducibility

(2014) Francis S. Collins et al.   NATURE

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

(2014) Mariel M. Finucane et al.   PLoS One

Scholarly Context Not Found: One in Five Articles Suffers from Reference Rot

(2014) Martin Klein et al.   PLoS One

An open investigation of the reproducibility of cancer biology research

(2014) Timothy M Errington et al.   eLife

All hail reproducibility in microbiome research

(2014) Jacques Ravel et al.   Microbiome

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

(2013) Alison Morris et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

A systematic review of the reporting of sample size calculations and corresponding data components in observational functional magnetic resonance imaging studies

(2013) Qing Guo et al.   NEUROIMAGE

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Correction: Small Protein-Mediated Quorum Sensing in a Gram-Negative Bacterium

(2013) Sang-Wook Han et al.   PLoS One

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

(2013) Daniel Garijo et al.   PLoS One

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retraction

(2013) S.-W. Lee et al.   SCIENCE

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

Reproducible Science

(2010) A. Casadevall et al.   INFECTION AND IMMUNITY

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

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

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

(2010) Sarah L. Kinnings et al.   PLoS Computational Biology

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

A Quick Guide to Organizing Computational Biology Projects

(2009) William Stafford Noble   PLoS Computational Biology

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

(2008) Ivaylo I. Ivanov et al.   Cell Host & Microbe

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE