Yohei Kondo

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All cells derive nutrition by absorbing some chemical and energy resources from the environment; these resources are used by the cells to reproduce the chemicals within them, which in turn leads to an increase in their volume. In this study we introduce a protocell model exhibiting catalytic reaction dynamics, energy metabolism, and cell growth. Results of(More)
We propose a statistical machine-learning approach to derive low-dimensional models by integrating noisy time-series data from partial observation of high-dimensional systems, aiming to utilize quantitative data on biological phenomena in the cell. In particular, the method estimates a model from data at different values of a bifurcation parameter in order(More)
Vascular endothelial function assessment yields important diagnostic and prognostic information on patients with (or at risk of) cardiovascular diseases. Flow-mediated dilation (FMD) is the most widely used noninvasive method for assessing the endothelial function. In this method, the magnitude of FMD is used as a surrogate marker for the endothelial(More)
A common strategy for sparse linear regression is to introduce regularization, which eliminates irrelevant features by letting the corresponding weights be zeros. However, regularization often shrinks the estimator for relevant features, which leads to incorrect feature selection. Motivated by the above-mentioned issue, we propose Bayesian masking (BM), a(More)
Cell-cell signaling is subject to variability in the extracellular volume, cell number, and dilution that potentially increase uncertainty in the absolute concentrations of the extracellular signaling molecules. To direct cell aggregation, the social amoebae Dictyostelium discoideum collectively give rise to oscillations and waves of cyclic adenosine(More)
Cells manage information encoded both in amplitude and frequency modulated signals (AM, FM). Biochemical networks processing these signals have to be able to extract infromation from the very noisy intracellular environment. The interactions between the different molecules and their properties (i.e. their sign and strength), determine the signal detection(More)
The biophysical framework of collective cell migration has been extensively investigated in recent years; however, it remains elusive how chemical inputs from neighboring cells are integrated to coordinate the collective movement. Here, we provide evidence that propagation waves of extracellular signal-related kinase (ERK) mitogen-activated protein kinase(More)