253 citations · 3k across the 163 of their papers we have counts for
14 papers · 1 filter
Entangled gene regulatory networks with cooperative expression endow robust adaptive responses to unforeseen environmental changes
Masayo Inoue, Kunihiko Kaneko
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Be…
Homeorhesis in Waddington's Landscape by Epigenetic Feedback Regulation
Yuuki Matsushita, Kunihiko Kaneko
In multicellular organisms, cells differentiate into several distinct types during early development. Determination of each cellular state, along with the ratio of each cell type,…
Epigenetic Ratchet: Spontaneous Adaptation via Stochastic Gene Expression
Yusuke Himeoka, Kunihiko Kaneko
Adaptation mechanism of cells on the basis of stochastic gene expression and epigenetic modification is proposed. From marginally stable states generated by epigenetic modification…
Cooperative reliable response from sloppy gene-expression dynamics
Masayo Inoue, Kunihiko Kaneko
Gene expression dynamics satisfying given input-output relationships were investigated by evolving the networks for an optimal response. We found three types of networks and corres…
Motif Analysis for Small-Number Effects in Chemical Reaction Dynamics
Nen Saito, Yuki Sughiyama, Kunihiko Kaneko
The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-…
Pluripotency, differentiation, and reprogramming: A gene expression dynamics model with epigenetic feedback regulation
Tadashi Miyamoto, Chikara Furusawa, Kunihiko Kaneko
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmenta…
Reciprocity Between Robustness of Period and Plasticity of Phase in Biological Clocks
Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
Circadian clocks exhibit the robustness of period and plasticity of phase against environmental changes such as temperature and nutrient conditions. Thus far, however, it is unclea…
Theoretical Analysis of Discreteness-Induced Transition in Autocatalytic Reaction Dynamics
Nen Saito, Kunihiko Kaneko
Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in molecule number have attracted much attention. Here, a method based on a Markov process wit…
Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration
Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is mai…
Robustness under functional constraint: The genetic network for temporal expression in Drosophila neurogenesis
Akihiko Nakajima, Takako Isshiki, Kunihiko Kaneko +1
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patte…
Network Evolution of Body Plans
Koichi Fujimoto, Shuji Ishihara, Kunihiko Kaneko
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear sim…
A generic mechanism for adaptive growth rate regulation
Chikara Furusawa, Kunihiko Kaneko
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells…
On Recursive Production and Evolvabilty of Cells: Catalytic Reaction Network Approach
Kunihiko Kaneko
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming…
Ubiquity of Log-normal Distributions in Intra-cellular Reaction Dynamic
Chikara Furusawa, Takao Suzuki, Akiko Kashiwagi +2
The discovery of two fundamental laws concerning cellular dynamics with recursive growth is reported. First, the chemical abundances measured over many cells are found to obey a lo…