A decomposition of a phylogenetically-informed distance into basal and terminal components.
Fukuyama.
A Consequentialist Critique of Binary Classification Evaluation Practices.
Flores, Schiff, Smith, Fukuyama, Wilson.
[arXiv]
Thrifty wide-context models of B cell receptor somatic hypermutation.
Sung, Johnson, Dumm, Simon, Haddox, Fukuyama, Matsen.
[eLife]
Inferring Mechanistic Parameters of Somatic Hypermutation Using Neural Networks and Approximate Bayesian Computation.
Fisher, Sung, Simon, Fukuyama*, Matsen*
Annals of Applied Statistics, 2025.
[link]
Determining whether weight status mediates the association between number of cigarettes smoked per day and all-cause mortality among US adults who smoke cigarettes.
Mestre, Zoh, Perry, Fukuyama, Parker.
PLoS ONE, 2025.
Calibrating dimension reduction hyperparameters in the presence of noise.
Lin and Fukuyama.
PLoS Computational Biology, 2024.
[link]
A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed beta-diversity measures.
Zhai and Fukuyama
PLoS Computational Biology, 2023.
[link]
Multiscale analysis of count data through topic alignment.
Fukuyama*, Symul*, Sankaran*.
Biostatistics, 2023.
[link] [arXiv] [package]
Local biplots for multidimensional scaling, with application to the microbiome
Fukuyama.
Journal of Computational and Graphical Statistics, 2022.
[link] [package] [example]
Lack of evidence for a substantial rate of templated mutagenesis in B cell diversification.
Fukuyama, Olson, Matsen.
Journal of Immunology, 2020.
[link] [PyMotifFinder] [scripts]
Leveraging big data to understand the interaction of task and language during monologic spoken discourse in speakers with and without aphasia.
Stark and Fukuyama.
Language, Cognition, and Neuroscience, 2020.
[link] [scripts]
Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances.
Fukuyama.
Genome Biology, 2019.
[link]
Adaptive gPCA: A method for structured dimensionality reduction.
Fukuyama.
Annals of Applied Statistics, 2019.
[link], [arXiv] [package]
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]
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]
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]
