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

mBio, 2018-06, Vol.9 (3)

2018

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Dynamics and associations of microbial community types across the human body

Nature (London), 2014-05, Vol.509 (7500), p.357-360

2014

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The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies

PLoS computational biology, 2010-07, Vol.6 (7), p.e1000844-e1000844

2010

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Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

PloS one, 2011-12, Vol.6 (12), p.e27310

2011

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A high-throughput DNA sequence aligner for microbial ecology studies

PloS one, 2009-12, Vol.4 (12), p.e8230-e8230

2009

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Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters

mSphere, 2021-08, Vol.6 (4), p.e0019121-e0019121

2021

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

mBio, 2016-08, Vol.7 (4)

2016

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Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

Applied and Environmental Microbiology, 2011-05, Vol.77 (10), p.3219-3226

2011

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Metabolic reconstruction for metagenomic data and its application to the human microbiome

PLoS computational biology, 2012-06, Vol.8 (6), p.e1002358-e1002358

2012

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Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

Applied and Environmental Microbiology, 2013-09, Vol.79 (17), p.5112-5120

2013

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Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

Applied and Environmental Microbiology, 2005-03, Vol.71 (3), p.1501-1506

2005

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De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

PeerJ (San Francisco, CA), 2015-12, Vol.3, p.e1487-e1487, Article e1487

2015

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Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

mBio, 2015-07, Vol.6 (4), p.e00974-e00974

2015

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Reintroducing mothur: 10 Years Later

Applied and environmental microbiology, 2020-01, Vol.86 (2)

2020

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Toward a census of bacteria in soil

PLoS computational biology, 2006-07, Vol.2 (7), p.e92-e92

2006

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A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

mBio, 2020-06, Vol.11 (3)

2020

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Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

mSphere, 2024-02, Vol.9 (2), p.e0035423-e0035423

2024

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Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

mBio, 2018-11, Vol.9 (6)

2018

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The gut microbiome modulates colon tumorigenesis

mBio, 2013-11, Vol.4 (6), p.e00692

2013

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The human gut microbiome as a screening tool for colorectal cancer

Cancer prevention research (Philadelphia, Pa.), 2014-11, Vol.7 (11), p.1112-1121

2014

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The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data

mSphere, 2019-05, Vol.4 (3)

2019

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NLRP6 Protects Il10−/− Mice from Colitis by Limiting Colonization of Akkermansia muciniphila

Cell reports (Cambridge), 2017-04, Vol.19 (4), p.733-745

2017

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Mathematical modeling of primary succession of murine intestinal microbiota

Proceedings of the National Academy of Sciences - PNAS, 2014-01, Vol.111 (1), p.439-444

2014

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Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures

Applied and Environmental Microbiology, 2006-10, Vol.72 (10), p.6773-6779

2006

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Status of the Microbial Census

Microbiology and Molecular Biology Reviews, 2004-12, Vol.68 (4), p.686-691

2004

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

Dynamics and associations of microbial community types across the human body

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

A high-throughput DNA sequence aligner for microbial ecology studies

Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters

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

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

Metabolic reconstruction for metagenomic data and its application to the human microbiome

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

Reintroducing mothur: 10 Years Later

Toward a census of bacteria in soil

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

The gut microbiome modulates colon tumorigenesis

The human gut microbiome as a screening tool for colorectal cancer

The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data

NLRP6 Protects Il10−/− Mice from Colitis by Limiting Colonization of Akkermansia muciniphila

Mathematical modeling of primary succession of murine intestinal microbiota

Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures

Status of the Microbial Census

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