Boolean modeling: a logic‐based dynamic approach for understanding signaling and regulatory networks and for making useful predictions
The biomolecules inside or near cells form a complex interacting system. Cellular
phenotypes and behaviors arise from the totality of interactions among the components of …
phenotypes and behaviors arise from the totality of interactions among the components of …
[PDF][PDF] A comparative study of qualitative and quantitative dynamic models of biological regulatory networks
A Saadatpour, R Albert - EPJ Nonlinear Biomedical Physics, 2016 - Springer
Background Mathematical modeling of biological regulatory networks provides valuable
insights into the structural and dynamical properties of the underlying systems. While …
insights into the structural and dynamical properties of the underlying systems. While …
Identifying (un) controllable dynamical behavior in complex networks
We present a technique applicable in any dynamical framework to identify control-robust
subsets of an interacting system. These robust subsystems, which we call stable modules …
subsets of an interacting system. These robust subsystems, which we call stable modules …
Estimating attractor reachability in asynchronous logical models
Logical models are well-suited to capture salient dynamical properties of regulatory
networks. For networks controlling cell fate decisions, cell fates are associated with model …
networks. For networks controlling cell fate decisions, cell fates are associated with model …
Introducing fuzzy reactive graphs: a simple application on biology
R Santiago, MA Martins, D Figueiredo - Soft Computing, 2021 - Springer
In this paper, we propose a generalization for fuzzy graphs in order to model reactive
systems with fuzziness. As we will show, the resulting fuzzy structure, called fuzzy reactive …
systems with fuzziness. As we will show, the resulting fuzzy structure, called fuzzy reactive …
Introduction to focus issue: quantitative approaches to genetic networks
All cells of living organisms contain similar genetic instructions encoded in the organism's
DNA. In any particular cell, the control of the expression of each different gene is regulated …
DNA. In any particular cell, the control of the expression of each different gene is regulated …
A yeast cell cycle pulse generator model shows consistency with multiple oscillatory and checkpoint mutant datasets
Modeling biological systems holds great promise for speeding up the rate of discovery in
systems biology by predicting experimental outcomes and suggesting targeted …
systems biology by predicting experimental outcomes and suggesting targeted …
Limit cycle analysis of a class of hybrid gene regulatory networks
H Sun, M Folschette, M Magnin - International Conference on …, 2022 - Springer
Many gene regulatory networks have periodic behavior, for instance the cell cycle or the
circadian clock. Therefore, the study of formal methods to analyze limit cycles in …
circadian clock. Therefore, the study of formal methods to analyze limit cycles in …
Single molecules can operate as primitive biological sensors, switches and oscillators
RD Hernansaiz-Ballesteros, L Cardelli… - BMC systems …, 2018 - Springer
Background Switch-like and oscillatory dynamical systems are widely observed in biology.
We investigate the simplest biological switch that is composed of a single molecule that can …
We investigate the simplest biological switch that is composed of a single molecule that can …
On Hybrid Gene Regulatory Networks
A Wurm, H Sun - arXiv preprint arXiv:2404.16197, 2024 - arxiv.org
In this work, we study a class of hybrid dynamical systems called hybrid gene regulatory
networks (HGRNs) which was proposed to model gene regulatory networks. In HGRNs …
networks (HGRNs) which was proposed to model gene regulatory networks. In HGRNs …