相关论文: Analytic stability analysis of three-component sel…
A repressilator consists of a loop made up of three repressively interacting genes. We construct a hexagonal lattice with repressilators on each triangle, and use this as a model system for multiple interacting feedback loops. Using…
In this research, we study biological networks at different scales: a gene autoregulatory network at the single-cell level and the gut microbiota at the population level. Proteins are the main actors in cells, they are the building blocks,…
Background: MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human…
Benchmark rankings are routinely used to justify scientific claims about method quality in gene regulatory network (GRN) inference, yet the stability of these rankings under plausible evaluation protocol choices is rarely examined. We…
We propose a new procedure to monitor and forecast the onset of transitions in high dimensional complex systems. We describe our procedure by an application to the Tangled Nature model of evolutionary ecology. The quasi-stable…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
This paper describes a simplified model of an electric circuit with a DC-DC converter and a PID-regulator as a system of integral differential equations with an identically singular matrix multiplying the higher derivative of the desired…
Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many…
Cellular decision-making (CDM) is a dynamic phenomenon often controlled by regulatory networks defining interactions between genes and transcription factor proteins. Traditional studies have focussed on molecular switches such as positive…
If one wants to explore the properties of a dynamical system systematically one has to be able to track equilibria and periodic orbits regardless of their stability. If the dynamical system is a controllable experiment then one approach is…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
A detailed stochastic model of single-gene auto-regulation is established and its solutions are explored when mRNA dynamics is fast compared with protein dynamics and in the opposite regime. The model includes all the sources of randomness…
Motivated by questions in biology, we investigate the stability of equilibria of the dynamical system $\mathbf{x}^{\prime}=P(t)\nabla f(x)$ which arise as critical points of $f$, under the assumption that $P(t)$ is positive semi-definite.…
Previous analytical studies of on-line Independent Component Analysis (ICA) learning rules have focussed on asymptotic stability and efficiency. In practice the transient stages of learning will often be more significant in determining the…
Discerning how a mutation affects the stability of a protein is central to the study of a wide range of diseases. Machine learning and statistical analysis techniques can inform how to allocate limited resources to the considerable time and…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
Robust simulation is essential for reliable operation and planning of transmission and distribution power grids. At present, disparate methods exist for steady-state analysis of the transmission (power flow) and distribution power grid…
The plant to be stabilized is a system node $\Sigma$ with generating triple $(A,B,C)$ and transfer function $\bf G$, where $A$ generates a contraction semigroup on the Hilbert space $X$. The control and observation operators $B$ and $C$ may…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…
In biochemical networks, complex dynamical features such as superlinear growth and oscillations are classically considered a consequence of autocatalysis. For the large class of parameter-rich kinetic models, which includes Generalized Mass…