Related papers: Regulatory patterns in molecular interaction netwo…
We obtain the phase diagram of random Boolean networks with nested canalizing functions. Using the annealed approximation, we obtain the evolution of the number $b_t$ of nodes with value one, and the network sensitivity $\lambda$, and we…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Formation of a molecular network from multifunctional precursors is modelled with a random graph process. The random graph model favours reactivity for monomers that are positioned close in the network topology, and disfavours reactivity…
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…
We formulate general rules for a coarse-graining of the dynamics, which we term `symbolic dynamics', of feedback networks with monotone interactions, such as most biological modules. Networks which are more complex than simple cyclic…
Understanding how the structure of within-system interactions affects the dynamics of the system is important in many areas of science. We extend a network dynamics modeling platform DSGRN, which combinatorializes both dynamics and…
We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E.coli. In order to identify the modular structure we introduce clustering…
In this paper, we propose a mean-field model which attempts to bridge the gap between random Boolean networks and more realistic stochastic modeling of genetic regulatory networks. The main idea of the model is to replace all regulatory…
High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
The behavior of the network and its stability are governed by both dynamics of individual nodes as well as their topological interconnections. Attention mechanism as an integral part of neural network models was initially designed for…
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…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…
Regulatory networks depict promoting or inhibiting interactions between molecules in a biochemical system. We introduce a category-theoretic formalism for regulatory networks, using signed graphs to model the networks and signed functors to…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…