Related papers: Towards Application of the RBNK Model
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
The genetic algorithm is an optimization procedure motivated by biological evolution and is successfully applied to optimization problems in different areas. A statistical mechanics model for its dynamics is proposed based on the…
Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Lots of bio-inspired research works have been conducted in self-adaptive software. They have focused on the external behavior of biological entities without their genetic material that causes this behavior and constitutes the challenge this…
Predicting how the brain can be driven to specific states by means of internal or external control requires a fundamental understanding of the relationship between neural connectivity and activity. Network control theory is a powerful tool…
The field of computational modeling of the brain is advancing so rapidly that now it is possible to model large scale networks representing different brain regions with a high level of biological detail in terms of numbers and synapses. For…
The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…
The concept of robustness of regulatory networks has been closely related to the nature of the interactions among genes, and the capability of pattern maintenance or reproducibility. Defining this robustness property is a challenging task,…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
Gene Regulatory Networks (GRNs) are intricate biological systems that control gene expression and regulation in response to environmental and developmental cues. Advances in computational biology, coupled with high throughput sequencing…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
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…
In this work, we present a quantum circuit model for inferring gene regulatory networks (GRNs). The model is based on the idea of using qubit-qubit entanglement to simulate interactions between genes. We provide preliminary results that…
Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…