Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies. - Julia Fukuyama; Paul J. McMurdie; Les Dethlefsen; David A. Relman; Susan P. Holmes (Pacific Symposium on Biocomputing, 2012)

phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data. - Paul J. McMurdie; Susan P. Holmes (Pacific Symposium on Biocomputing, 2012)

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. - Paul J. McMurdie; Susan P. Holmes (PLoS Comput. Biol., 2014)

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking. - Paul J. McMurdie; Susan P. Holmes (Bioinform., 2015)