Julia Fukuyama
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Explore the profile of Julia Fukuyama including associated specialties, affiliations and a list of published articles.
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15
Citations
580
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Recent Articles
1.
Sung K, Johnson M, Dumm W, Simon N, Haddox H, Fukuyama J, et al.
bioRxiv
. 2024 Dec;
PMID: 39651125
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, for understanding the selective forces guiding affinity maturation, and...
2.
Lin J, Fukuyama J
PLoS Comput Biol
. 2024 Sep;
20(9):e1012427.
PMID: 39264943
The goal of dimension reduction tools is to construct a low-dimensional representation of high-dimensional data. These tools are employed for a variety of reasons such as noise reduction, visualization, and...
3.
Zhai H, Fukuyama J
PLoS Comput Biol
. 2023 Jan;
19(1):e1010821.
PMID: 36608056
k-mer-based distances are often used to describe the differences between communities in metagenome sequencing studies because of their computational convenience and history of effectiveness. Although k-mer-based distances do not use...
4.
Fukuyama J, Sankaran K, Symul L
Biostatistics
. 2022 Jun;
24(4):1045-1065.
PMID: 35657012
Topic modeling is a popular method used to describe biological count data. With topic models, the user must specify the number of topics $K$. Since there is no definitive way...
5.
Fukuyama J, Olson B, Matsen 4th F
J Immunol
. 2020 Jul;
205(4):936-944.
PMID: 32669310
BCR sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major contributor to somatic hypermutation and therefore Ig...
6.
Fukuyama J
Genome Biol
. 2019 Jun;
20(1):131.
PMID: 31253178
Background: Phylogenetically informed distances are commonly used in the analysis of microbiome data, and analysts have many options to choose from. Although all phylogenetic distances share the goal of incorporating...
7.
Fukuyama J, Rumker L, Sankaran K, Jeganathan P, Dethlefsen L, Relman D, et al.
PLoS Comput Biol
. 2017 Aug;
13(8):e1005706.
PMID: 28821012
Our work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like disturbances that eliminate most gastrointestinal biomass can be...
8.
Vendrame E, Fukuyama J, Strauss-Albee D, Holmes S, Blish C
Cytometry B Clin Cytom
. 2016 Dec;
92(1):57-67.
PMID: 27933717
Background: Natural killer (NK) cells have antiviral and antitumor activity that could be harnessed for the treatment of infections and malignancies. To maintain cell viability and enhance antiviral and antitumor...
9.
Callahan B, Proctor D, Relman D, Fukuyama J, Holmes S
Pac Symp Biocomput
. 2016 Jan;
21:183-94.
PMID: 26776185
This article presents a reproducible research workflow for amplicon-based microbiome studies in personalized medicine created using Bioconductor packages and the knitr markdown interface.We show that sometimes a multiplicity of choices...
10.
Strauss-Albee D, Fukuyama J, Liang E, Yao Y, Jarrell J, Drake A, et al.
Sci Transl Med
. 2015 Jul;
7(297):297ra115.
PMID: 26203083
Innate natural killer (NK) cells are diverse at the single-cell level because of variegated expressions of activating and inhibitory receptors, yet the developmental roots and functional consequences of this diversity...