Paul J. McMurdie

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Exact sequence variants should replace operational taxonomic units in marker gene data analysis

Benjamin J. Callahan, Paul J. McMurdie, Susan Holmes, 2017 .

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

Susan Holmes, Paul J. McMurdie, S. Holmes, 2013, PloS one.

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

Susan P. Holmes, Paul J. McMurdie, S. Holmes, 2014, Bioinform..

Waste Not , Want Not : Why Rarefying Microbiome Data is Inadmissible . October 1 , 2013

Susan P. Holmes, Paul J. McMurdie, S. Holmes, 2013 .

Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies

Susan P. Holmes, Les Dethlefsen, Paul J. McMurdie, 2011, Pacific Symposium on Biocomputing.

phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data

Susan P. Holmes, Paul J. McMurdie, S. Holmes, 2011, Pacific Symposium on Biocomputing.

DADA2: High resolution sample inference from amplicon data

Susan Holmes, Benjamin J. Callahan, Paul J. McMurdie, 2015, bioRxiv.

Unusual Codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides Species

Susan Holmes, Paul J. McMurdie, Alfred M. Spormann, 2007, Applied and Environmental Microbiology.

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

Paul J. McMurdie, A. Lapidus, A. Spormann, 2009, PLoS genetics.

DADA2: High resolution sample inference from Illumina amplicon data

Paul J. McMurdie, S. Holmes, B. Callahan, 2016, Nature Methods.

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

Paul J. McMurdie, S. Holmes, B. Callahan, 2017, The ISME Journal.

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease

Aldert L. Zomer, Paul J. McMurdie, J. Bell, 2020, Nature Communications.

Temporal and spatial variation of the human microbiota during pregnancy

Christine L. Sun, Paul J. McMurdie, Daniel B. DiGiulio, 2015, Proceedings of the National Academy of Sciences.

Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation

James H. Bullard, Paul J. McMurdie, P. McMurdie, 2020, BMJ open diabetes research & care.

Advancing our understanding of the human microbiome using QIIME.

Rob Knight, Donna Berg-Lyons, James Huntley, 2013, Methods in enzymology.

Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease

Paul J. McMurdie, P. McMurdie, N. Justice, 2021, Gut microbes.

Increased circulating butyrate and ursodeoxycholate during probiotic intervention in humans with type 2 diabetes

Connor T. Skennerton, Paul J. McMurdie, P. McMurdie, 2022, BMC microbiology.

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

Paul J. McMurdie, S. Holmes, B. Callahan, 2016, F1000Research.

Normalization of Microbiome Profiling Data.

Paul J. McMurdie, Paul J McMurdie, 2018, Methods in molecular biology.

Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer

Paul J. McMurdie, T. DeSantis, P. McMurdie, 2017, Gut.

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

Paul J. McMurdie, S. Holmes, 2013, PloS one.

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Paul J. McMurdie, S. Holmes, 2013, PLoS Comput. Biol..

Monitoring Abundance and Expression of “Dehalococcoides” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column

Paul J. McMurdie, A. Spormann, L. Semprini, 2008, Applied and Environmental Microbiology.

Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides

Paul J. McMurdie, L. Hug, A. Spormann, 2011, BMC Genomics.