Related papers: Digital clocks: simple Boolean models can quantita…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
Many biological processes display oscillatory behavior based on an approximately 24 hour internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…
We study the impact of light on the mammalian circadian system using the theory of phase response curves. Using a recently developed ansatz we derive a low-dimensional macroscopic model for the core circadian clock in mammals.…
The circadian rhythm plays a crucial role in regulating biological processes, and its disruption is linked to various health issues. Identifying small molecules that influence the circadian period is essential for developing targeted…
The mammalian circadian system comprises a network of cell-autonomous oscillators, spanning from the central clock in the brain to peripheral clocks in other organs. These clocks are tightly coordinated to orchestrate rhythmic physiological…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
Complex systems are often modeled as Boolean networks in attempts to capture their logical structure and reveal its dynamical consequences. Approximating the dynamics of continuous variables by discrete values and Boolean logic gates may,…
A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…
Boolean networks constitute relevant mathematical models to study the behaviours of genetic and signalling networks. These networks define regulatory influences between molecular nodes, each being associated to a Boolean variable and a…
The cosinor model is frequently used to represent the oscillatory behavior of different genes over time. When data are collected from multiple individuals, the cosinor model is estimated with recorded gene expression levels and the 24 hour…
Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a…
Circadian (~24hr) clocks are self-sustained endogenous oscillators with which organisms keep track of daily and seasonal time. Circadian clocks frequently rely on interlocked transcriptional- translational feedback loops to generate rhythms…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian…
Periodic forcing of nonlinear oscillators leads to a large number of dynamic behaviors. The coupling of the cell-cycle to the circadian clock provides a biological realization of such forcing. Using high throughput single-cell microscopy,…
To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24h period. Yet, a limit-cycle oscillator is not…
Self-sustaining nonlinear oscillators of practically any type can function as latches and registers if Boolean logic states are represented physically as the phase of oscillatory signals. Combinational operations on such phase-encoded logic…
A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has…
This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The…