Environmental sensing, information transfer, and cellular decision-making

CG Bowsher, PS Swain - Current opinion in biotechnology, 2014 - Elsevier
The recognition that gene expression can be substantially stochastic poses the question of
how cells respond to dynamic environments using biochemistry that itself fluctuates. The …

Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior

PL Freddolino, S Tavazoie - Annual review of cell and …, 2012 - annualreviews.org
Microbial regulatory strategies have long been understood in terms of the homeostatic
framework, in which a response is interpreted as a restoring force counteracting the …

Decisions on the fly in cellular sensory systems

ED Siggia, M Vergassola - Proceedings of the National …, 2013 - National Acad Sciences
Cells send and receive signals through pathways that have been defined in great detail
biochemically, and it is often presumed that the signals convey only level information. Cell …

A Markovian approach to the optimal demodulation of diffusion-based molecular communication networks

CT Chou - IEEE Transactions on Communications, 2015 - ieeexplore.ieee.org
In a diffusion-based molecular communication network, transmitters and receivers
communicate by using signalling molecules (or ligands) in a fluid medium. This paper …

Maximum A-Posteriori Decoding for Diffusion-Based Molecular Communication Using Analog Filters

CT Chou - IEEE Transactions on Nanotechnology, 2015 - ieeexplore.ieee.org
Molecular communication is a promising approach to realize the communication between
nanoscale devices. In a diffusion-based molecular communication network, transmitters and …

Theoretical aspects of cellular decision-making and information-processing

TJ Kobayashi, A Kamimura - Advances in Systems Biology, 2012 - Springer
Microscopic biological processes have extraordinary complexity and variety at the sub-
cellular, intra-cellular, and multi-cellular levels. In dealing with such complex phenomena …

Detection of persistent signals and its relation to coherent feed-forward loops

CT Chou - Royal Society open science, 2018 - royalsocietypublishing.org
Many studies have shown that cells use the temporal dynamics of signalling molecules to
encode information. One particular class of temporal dynamics is persistent and transient …

Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity

MK Kajita, K Aihara, TJ Kobayashi - Physical Review E, 2017 - APS
Specific interactions between receptors and their target ligands in the presence of nontarget
ligands are crucial for biological processes such as T cell ligand discrimination. To …

Mapping, modeling, and reprogramming cell-fate decision making systems

L Ham, TE Woodford, MA Coomer… - arXiv preprint arXiv …, 2024 - arxiv.org
Many cellular processes involve information processing and decision making. We can probe
these processes at increasing molecular detail. The analysis of heterogeneous data remains …

[HTML][HTML] Stability analysis for the cellular signaling systems composed of two phosphorylation-dephosphorylation cyclic reactions

C Sueyoshi, T Naka - Computational Molecular Bioscience, 2017 - scirp.org
The regulatory mechanisms in cellular signaling systems have been studied intensively from
the viewpoint that the malfunction of the regulation is thought to be one of the substantial …