17 Publications
2022
Multiscale analysis of count data through topic alignment.
Fukuyama, Julia⋅Sankaran, Kris and Symul, Laura
Biostatistics (Oxford, England), June 2, 2022. | Journal Article
2021
Leveraging big data to understand the interaction of task and language during monologic spoken discourse in speakers with and without aphasia
Stark, Brielle C⋅Stark, Brielle C⋅Fukuyama, Julia and Fukuyama, Julia
Language, Cognition and Neuroscience, vol. 36, (no. 5), pp. 562-585, Jun 2021. | Journal Article
2020
Lack of Evidence for a Substantial Rate of Templated Mutagenesis in B Cell Diversification.
Fukuyama, Julia⋅Olson, Branden J and Matsen, Frederick A
Journal of immunology (Baltimore, Md. : 1950), vol. 205, (no. 4), pp. 936-944, August 15, 2020. | Journal Article
2019
Adaptive gPCA: A method for structured dimensionality reduction with applications to microbiome data
Fukuyama, Julia
The Annals of Applied Statistics, vol. 13, (no. 2), pp. 1067, 2019-06-00. | Journal Article
 
Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances
Fukuyama, Julia
Genome Biology, vol. 20, (no. 1), pp. 131, 2019-12-00. | Journal Article
2018
A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow
Proctor, Diana M⋅Proctor, Diana⋅Proctor, Diana M⋅Fukuyama, Julia⋅Fukuyama, Julia A⋅Fukuyama, Julia A⋅Loomer, Peter M⋅Loomer, Peter⋅Loomer, Peter M⋅Armitage, Gary⋅Armitage, Gary C⋅Armitage, Gary C⋅Lee, Stacey⋅Lee, Stacey A⋅Lee, Stacey A⋅Davis, Nicole⋅Davis, Nicole M⋅Davis, Nicole M⋅Ryder, Mark I⋅Ryder, Mark⋅Ryder, Mark I⋅Holmes, Susan P⋅Holmes, Susan P⋅Holmes, Susan⋅Relman, David A⋅Relman, David and Relman, David A
Nature communications, vol. 9, (no. 1), pp. 10, 2018-02-14. | Journal Article
2017
Adaptive gPCA: A method for structured dimensionality reduction
Fukuyama, Julia
2017-02-01. | Journal Article
 
Mass Cytometry Analytical Approaches Reveal Cytokine-Induced Changes in Natural Killer Cells
Vendrame, Elena⋅Vendrame, Elena⋅Vendrame, Elena⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Strauss-Albee, Dara M⋅Strauss-Albee, Dara M⋅Strauss-Albee, Dara M.⋅Holmes, Susan⋅Holmes, Susan⋅Holmes, Susan⋅Blish, Catherine A⋅Blish, Catherine A. and Blish, Catherine A
Cytometry Part B: Clinical Cytometry, vol. 92, (no. 1), pp. 67, 2017-01-00. | Journal Article
 
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
Fukuyama, Julia⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Rumker, Laurie⋅Rumker, Laurie⋅Rumker, Laurie⋅Sankaran, Kris⋅Sankaran, Kris⋅Sankaran, Kris⋅Jeganathan, Pratheepa⋅Jeganathan, Pratheepa⋅Jeganathan, Pratheepa⋅Dethlefsen, Les⋅Dethlefsen, Les⋅Dethlefsen, Les⋅Relman, David A⋅Relman, David A⋅Relman, David A⋅Holmes, Susan P⋅Holmes, Susan P and Holmes, Susan P
PLoS computational biology, vol. 13, (no. 8), pp. e1005706, 2017-Aug. | Journal Article
2016
Bioconductor workflow for microbiome data analysis: from raw reads to community analyses
Callahan, Ben J⋅Callahan, Ben J⋅Sankaran, Kris⋅Sankaran, Kris⋅Fukuyama, Julia A⋅Fukuyama, Julia A⋅McMurdie, Paul J⋅McMurdie, Paul J⋅Holmes, Susan P and Holmes, Susan P
F1000Research, vol. 5, pp. 1492, 2016-00-00. | Journal Article
 
REPRODUCIBLE RESEARCH WORKFLOW IN R FOR THE ANALYSIS OF PERSONALIZED HUMAN MICROBIOME DATA
Callahan, Benjamin⋅Callahan, Benjamin⋅Proctor, Diana⋅Proctor, Diana⋅Relman, David⋅Relman, David⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Holmes, Susan and Holmes, Susan
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, vol. 21, pp. 194, 2016-00-00. | Journal Article
2015
Human NK cell repertoire diversity reflects immune experience and correlates with viral susceptibility
Strauss-Albee, Dara M⋅Strauss-Albee, Dara M⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Liang, Emily C⋅Liang, Emily C⋅Yao, Yi⋅Yao, Yi⋅Jarrell, Justin A⋅Jarrell, Justin A⋅Drake, Alison L⋅Drake, Alison L⋅Kinuthia, John⋅Kinuthia, John⋅Montgomery, Ruth R⋅Montgomery, Ruth R⋅John-Stewart, Grace⋅John-Stewart, Grace⋅Holmes, Susan⋅Holmes, Susan⋅Blish, Catherine A and Blish, Catherine A
Science translational medicine, vol. 7, (no. 297), pp. 297ra115, 2015-Jul-22. | Journal Article
 
Pregnancy Does Not Attenuate the Antibody or Plasmablast Response to Inactivated Influenza Vaccine
Kay, Alexander W⋅Kay, Alexander W⋅Bayless, Nicholas L⋅Bayless, Nicholas L⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Aziz, Natali⋅Aziz, Natali⋅Dekker, Cornelia L⋅Dekker, Cornelia L⋅Mackey, Sally⋅Mackey, Sally⋅Swan, Gary E⋅Swan, Gary E⋅Davis, Mark M⋅Davis, Mark M⋅Blish, Catherine A and Blish, Catherine A
The Journal of infectious diseases, vol. 212, (no. 6), pp. 870, 2015-Sep-15. | Journal Article
2014
Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy
Kay, Alexander W⋅Kay, Alexander⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Aziz, Natali⋅Aziz, Natali⋅Dekker, Cornelia L⋅Dekker, Cornelia⋅Mackey, Sally⋅Mackey, Sally⋅Swan, Gary E⋅Swan, Gary⋅Davis, Mark M⋅Davis, Mark⋅Holmes, Susan⋅Holmes, Susan⋅Blish, Catherine and Blish, Catherine A
Proceedings of the National Academy of Sciences of the United States of America, vol. 111, (no. 40), pp. 14511, 20141007. | Journal Article
2013
Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage
Yan, Miling⋅Yan, Miling⋅Pamp, Sünje J⋅Pamp, Sünje Johanna⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Hwang, Peter H⋅Hwang, Peter H⋅Cho, Do-Yeon⋅Cho, Do-Yeon⋅Holmes, Susan⋅Holmes, Susan⋅Relman, David A and Relman, David A
Cell Host & Microbe, vol. 14, (no. 6), pp. 640, 2013-12-11. | Journal Article
2012
Comparisons of distance methods for combining covariates and abundances in microbiome studies
Fukuyama, Julia⋅Fukuyama, Julia⋅McMurdie, Paul J⋅McMurdie, Paul J⋅Dethlefsen, Les⋅Dethlefsen, Les⋅Relman, David A⋅Relman, David A⋅Holmes, Susan and Holmes, Susan
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 224, 2012-00-00. | Journal Article
2007
Thrombospondin-1 Inhibits Nitric Oxide Signaling via CD36 by Inhibiting Myristic Acid Uptake
Isenberg, Jeffrey⋅Isenberg, Jeff⋅Jia, Yifeng⋅Jia, Yifeng⋅Fukuyama, Julia⋅Fukuyama, Julia⋅Switzer, Christopher H⋅Switzer, Christopher⋅Wink, David A⋅Wink, David⋅Roberts, David and Roberts, David D
Journal of Biological Chemistry, vol. 282, (no. 21), pp. 15415, 20070525. | Journal Article