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)

Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data. - Benjamin J. Callahan; Diana Proctor; David A. Relman; Julia Fukuyama; Susan P. Holmes (PSB, 2016)

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. - Julia Fukuyama; Laurie Rumker; Kris Sankaran; Pratheepa Jeganathan; Les Dethlefsen; David A. Relman; Susan P. Holmes (PLoS Comput. Biol., 2017)

Local biplots for multidimensional scaling, with application to the microbiome. - Julia Fukuyama (J. Comput. Graph. Stat., 2022)

A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures. - Hongxuan Zhai; Julia Fukuyama (PLoS Comput. Biol., 2023)

Calibrating dimension reduction hyperparameters in the presence of noise. - Justin Lin; Julia Fukuyama (PLoS Comput. Biol., 2024)