Disentangling the growth curve of microbial culture
Daiki Kumakura, Ryo Yamaguchi, Akane Hara, Shinji Nakaoka
Publication recordDaiki Kumakura
I am a mathematical biologist with a Ph.D. in Life Science. Since April 2025, I have worked as a bioinformatics researcher in the pharmaceutical industry.
My research has examined microbial growth, antibiotic response and resistance, and changes in microbial communities using mathematical models and data analysis. In pharmaceutical research, this work connects particularly to pharmacometrics.
Selected publications
A prototype coupled modeling approach for predicting harmful algal blooms: A case study in Chile
Ishara Uhanie Perera, So Fujiyoshi, Daiki Kumakura, Carolina Medel, Kyoko Yarimizu, Osvaldo Artal, Pablo Reche, Oscar Espinoza-González, Leonardo Guzman, Felipe Tucca, Alexander Jaramillo-Torres, Jacquelinne J. Acuña, Milko A. Jorquera, Shinji Nakaoka, Satoshi Nagai, Fumito Maruyama
Publication recordSoftware
RLR_transform
R scripts exploring transformations of compositional time series and dynamic interaction inference using convergent cross mapping (CCM), including simulations and figure-generation code.
CRiSM
A Python CLI connecting marker-gene discovery and extraction from genomes with alignment, sequence concatenation, and phylogenetic inference.