Research

Microbiome papers

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow.
Proctor, Fukuyama, Loomer, Armitage, Lee, Davis, Ryder, Holmes, Relman.
Nature Communications, 2018.
[link]

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
Fukuyama*, Rumker*, Sankaran*, Jeganathan, Dethlefsen, Relman, Holmes.
PLoS Computational Biology, 2017.
[link]

Bioconductor workflow for microbiome data analysis: from raw reads to community analyses.
Callahan, Sankaran, Fukuyama, McMurdie, Holmes.
F1000Research, 2016.
[link]

Reproducible research workflow in R for the analysis of personalized human microbiome data.
Callahan, Proctor, Fukuyama, Relman, Holmes.
Pacific Symposium on Biocomputing, 2016.
[link]

Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage.
Yan, Pamp, Fukuyama, Hwang, Cho, Holmes, Relman.
Cell Host and Microbe, 2013.
[link]

Comparisons of distance methods for combining covariates and abundances in microbiome studies.
Fukuyama, McMurdie, Dethlefsen, Relman, Holmes.
Pacific Symposium on Biocomputing, 2012.
[link]

Immunology papers

Mass cytometry analytical approaches reveal cytokine-induced changes in natural killer cells.
Vendrame*, Fukuyama*, Strauss-Albee, Holmes, Blish.
Cytometry Part B: Clinical Cytometry, 2016.
[link]

Human NK cell repertoire diversity reflects immune experience and correlates with viral susceptibility.
Strauss-Albee, Fukuyama, Liang, Yao, Jarrell, Drake, Kinuthia, Montgomery, John-Stewart, Holmes, Blish.
Science Translational Medicine, 2015.
[link]

Pregnancy does not attenuate the antibody or plasmablast response to inactivated influenza vaccine.
Kay, Bayless, Fukuyama, Aziz, Dekker, Mackey, Swan, Davis, Blish.
Journal of Infectious Diseases, 2015.
[link]

Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy.
Kay, Fukuyama, Aziz, Dekker, Mackey, Swan, Davis, Holmes, Blish.
Proceedings of the National Academy of Sciences, 2014.
[link]

Submitted

Adaptive gPCA: A method for structured dimensionality reduction.
Fukuyama.
[arXiv]