| Bioconductor workflow for microbiome data analysis: from raw reads to community analyses BJ Callahan, K Sankaran, JA Fukuyama, PJ McMurdie, SP Holmes F1000Research 5, 2016 | 1017 | 2016 |
| Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage M Yan, SJ Pamp, J Fukuyama, PH Hwang, DY Cho, S Holmes, ... Cell host & microbe 14 (6), 631-640, 2013 | 391 | 2013 |
| Human NK cell repertoire diversity reflects immune experience and correlates with viral susceptibility DM Strauss-Albee, J Fukuyama, EC Liang, Y Yao, JA Jarrell, AL Drake, ... Science translational medicine 7 (297), 297ra115-297ra115, 2015 | 199 | 2015 |
| Thrombospondin-1 inhibits nitric oxide signaling via CD36 by inhibiting myristic acid uptake JS Isenberg, Y Jia, J Fukuyama, CH Switzer, DA Wink, DD Roberts Journal of Biological Chemistry 282 (21), 15404-15415, 2007 | 155 | 2007 |
| A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow DM Proctor, JA Fukuyama, PM Loomer, GC Armitage, SA Lee, NM Davis, ... Nature communications 9 (1), 681, 2018 | 116 | 2018 |
| Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy AW Kay, J Fukuyama, N Aziz, CL Dekker, S Mackey, GE Swan, MM Davis, ... Proceedings of the National Academy of Sciences 111 (40), 14506-14511, 2014 | 110 | 2014 |
| Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment J Fukuyama, L Rumker, K Sankaran, P Jeganathan, L Dethlefsen, ... PLoS computational biology 13 (8), e1005706, 2017 | 72 | 2017 |
| Comparisons of distance methods for combining covariates and abundances in microbiome studies J Fukuyama, PJ McMurdie, L Dethlefsen, DA Relman, S Holmes Biocomputing 2012, 213-224, 2012 | 69 | 2012 |
| Pregnancy does not attenuate the antibody or plasmablast response to inactivated influenza vaccine AW Kay, NL Bayless, J Fukuyama, N Aziz, CL Dekker, S Mackey, ... The Journal of infectious diseases 212 (6), 861-870, 2015 | 59 | 2015 |
| Mass cytometry analytical approaches reveal cytokine‐induced changes in natural killer cells E Vendrame, J Fukuyama, DM Strauss‐Albee, S Holmes, CA Blish Cytometry Part B: Clinical Cytometry 92 (1), 57-67, 2017 | 46 | 2017 |
| Reproducible research workflow in R for the analysis of personalized human microbiome data B Callahan, D Proctor, D Relman, J Fukuyama, S Holmes Biocomputing 2016: Proceedings of the Pacific Symposium, 183-194, 2016 | 45 | 2016 |
| Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Res. 2016; 5: 1492 BJ Callahan, K Sankaran, JA Fukuyama, PJ McMurdie, SP Holmes | 34 | 2020 |
| Leveraging big data to understand the interaction of task and language during monologic spoken discourse in speakers with and without aphasia BC Stark, J Fukuyama Language, Cognition and Neuroscience 36 (5), 562-585, 2021 | 30 | 2021 |
| Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances J Fukuyama Genome biology 20, 1-16, 2019 | 25 | 2019 |
| Multiscale analysis of count data through topic alignment J Fukuyama, K Sankaran, L Symul Biostatistics 24 (4), 1045-1065, 2023 | 11 | 2023 |
| Adaptive gPCA: A method for structured dimensionality reduction J Fukuyama arXiv preprint arXiv:1702.00501, 2017 | 9 | 2017 |
| ADAPTIVE GPCA J Fukuyama The Annals of Applied Statistics 13 (2), 1043-1067, 2019 | 7 | 2019 |
| Local biplots for multidimensional scaling, with application to the microbiome J Fukuyama Journal of Computational and Graphical Statistics 31 (3), 779-789, 2022 | 2 | 2022 |
| Calibrating dimension reduction hyperparameters in the presence of noise J Lin, J Fukuyama PLOS Computational Biology 20 (9), e1012427, 2024 | 1 | 2024 |
| A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures H Zhai, J Fukuyama PLOS Computational Biology 19 (1), e1010821, 2023 | 1 | 2023 |