Stoichiometric Rays:
A simple method to compute the controllable set of enzymatic reaction systems

Yusuke Himeoka, Shuhei A. Horiguchi, and Tetsuya J. Kobayashi
arXiv:2403.02169, (2024)

Perturbation-response analysis of in silico metabolic dynamics:
Hard-coded responsiveness in the cofactor and network sparsity

Yusuke Himeoka and Chikara Furusawa
bioRxiv (doi:10.1101/2023.10.18.562862), (2023)

Evolution of hierarchy and irreversibility in theoretical cell differentiation model

Yoshiyuki T. Nakamura, Yusuke Himeoka, Nen Saito, and Chikara Furusawa
PNAS Nexus, 3, 1, 454, (2023)

Structural determinants of relaxation dynamics in chemical reaction networks

Yusuke Himeoka, Julius B. Kirkegaard,
Namiko Mitarai, and Sandeep Krishna
bioRxiv (doi:10.1101/2022.05.25.493374), (2022)

Emergence of growth and dormancy
from a kinetic model of the Escherichia coli central carbon metabolism

Yusuke Himeoka, and Namiko Mitarai
Physical Review Research 4, 043223 (2022) 

Distinct survival, growth lag, and ribosomal RNA degradation kinetics
during long-term starvation for carbon or phosphate

Yusuke Himeoka, Bertil Gummesson,
Michael A. Sørensen, Sine Lo Svenningsen, and Namiko Mitarai
mSphere, e01006-21., (2022)

When to wake up? The optimal waking-up strategies
for starvation-induced persistence

Yusuke Himeoka, and Namiko Mitarai
PLoS Computational Biology, 17(2):e1008655, (2021)

Dynamics of bacterial populations under the feast-famine cycles

Yusuke Himeoka, and Namiko Mitarai
Physical Review Research, 2, (2020), 013372

Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems:
post-segregational killing and noise filtering 

Yusuke Himeoka, and Namiko Mitarai
Physical Biology, 16, (2019), 026001

Epigenetic Ratchet: Spontaneous Adaptation via Stochastic Gene Expression

Yusuke Himeoka, and Kunihiko Kaneko
Scientific Reports, 10, 459, (2020)

Theory for Transitions Between Exponential and Stationary Phases:
Universal Laws for Lag Time

Yusuke Himeoka, and Kunihiko Kaneko 

Phys. Rev. X 7, 021049, (2017) 
(​F1000 Prime recommended)

Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: consequence of anti-phase coupling between reaction flux and affinity

Yusuke Himeoka, and Kunihiko Kaneko 

Physical biology 13.2 (2016)

Entropy production of a steady-growth cell with catalytic reactions

Yusuke Himeoka, and Kunihiko Kaneko
Phys. Rev. E 90, 042714 (2014)