Related papers: Characteristics of Molecular-biological Systems an…
This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…
Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a powerlaw distribution. While the degree distribution does not summarize all aspects of a network it has often been…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
A key problem in the study and design of complex systems is the apparent disconnection between the microscopic and the macroscopic. It is not straightforward to identify the local interactions that give rise to an observed global…
First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…
Synchronization processes in populations of locally interacting elements are in the focus of intense research in physical, biological, chemical, technological and social systems. The many efforts devoted to understand synchronization…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
The study of network representations of physical, biological, and social phenomena can help us better understand the structural and functional dynamics of their networks and formulate predictive models of these phenomena. However, due to…
A key step in the origin of life is the emergence of a primitive metabolism. This requires the formation of a subset of chemical reactions that is both self-sustaining and collectively autocatalytic. A generic theory to study such processes…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
Predicting missing links in complex networks requires algorithms that are able to explore statistical regularities in the existing data. Here we investigate the interplay between algorithm efficiency and network structures through the…
Graph theory provides a primary tool for analyzing and designing computer communication networks. In the past few decades, Graph theory has been used to study various types of networks, including the Internet, wide Area Networks, Local Area…
What is a complex network? How do we characterize complex networks? Which systems can be studied from a network approach? In this text, we motivate the use of complex networks to study and understand a broad panoply of systems, ranging from…
We give a self-contained introduction to the theory of directed graphs, leading up to the relationship between the Perron-Frobenius eigenvectors of a graph and its autocatalytic sets. Then we discuss a particular dynamical system on a fixed…
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…
Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs…