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.

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

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

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

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.

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

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.

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.

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.

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.


Adaptive gPCA: A method for structured dimensionality reduction.