Related papers: Hierarchical p-Adic Framework for Gene Regulatory …
In this note we describe instances where values of the $K$-theoretical regulator map evaluated on topological cycles equal entropies of topological actions by a group $\Gamma$. These entropies can also be described by determinants on the…
The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle…
Using a generalized random recurrent neural network model, and by extending our recently developed mean-field approach [J. Aljadeff, M. Stern, T. Sharpee, Phys. Rev. Lett. 114, 088101 (2015)], we study the relationship between the network…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
Turing instability in activator-inhibitor systems provides a paradigm of nonequilibrium pattern formation; it has been extensively investigated for biological and chemical processes. Turing pattern formation should furthermore be possible…
We solve the problem of identifying (reconstructing) network topology from steady state network measurements. Concretely, given only a data matrix $\mathbf{X}$ where the $X_{ij}$ entry corresponds to flow in edge $i$ in configuration…
Genes are connected in regulatory networks, often modelled by ordinary differential equations. Changes in expression of a gene propagate to other genes along paths in the network. At a stable state, the system's Jacobian matrix confers…
The mathematical basis of p-adic Higgs mechanism discussed in papers [email protected] 9410058-62 is considered in this paper. The basic properties of p-adic numbers, of their algebraic extensions and the so called canonical…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
The arithmetic regularity lemma for $\mathbb{F}_p^n$, proved by Green in 2005, states that given a subset $A\subseteq \mathbb{F}_p^n$, there exists a subspace $H\leq \mathbb{F}_p^n$ of bounded codimension such that $A$ is Fourier-uniform…
A self-regulatory genetic circuit, where a protein acts as a positive regulator of its own production, is known to be a simplest form of biological network with a positive feedback loop. Although at least three components, DNA, RNA, and the…
By embedding physical intuition, network architectures enforce fundamental properties, such as energy conservation laws, leading to plausible predictions. Yet, scaling these models to intrinsically high-dimensional systems remains a…
Parametric models abstract part of the specification of dynamical models by integral parameters. They are for example used in computational systems biology, notably with parametric regulatory networks, which specify the global architecture…
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…
The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
Detecting anomalous edges and nodes in dynamic networks is critical in various areas, such as social media, computer networks, and so on. Recent approaches leverage network embedding technique to learn how to generate node representations…
The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…
Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of…
Dominance hierarchy among animals is widespread in various species and believed to serve to regulate resource allocation within an animal group. Unlike small groups, however, detection and quantification of linear hierarchy in large groups…
Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…