McMurdie and Holmes (2014) Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible PLoS Computational Biology 10(4): e1003531
Presubmission versions ahead of acceptance (2013): PDF version 2, PDF version 1
McMurdie and Holmes (2014) Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking. Bioinformatics (Oxford, England) 31(2), 282–283.
McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217
The phyloseq project also has a number of supporting online resources, including (but probably not limited to)
I recommend checking this page, and the issues tracker, before posting new issues.
This is the recommended location to post
(1) feature requests (2) bug reports (3) theoretical considerations (4) other issues, feedback (5) ask for help
Search previous posts, and check the phyloseq FAQ before posting a new issue.