Related papers: Complex networks theory for analyzing metabolic ne…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyse the full hierarchical organisation of biochemical networks and is applied to 43 organisms…
Over the last two decades, network science has greatly advanced our understanding of how the collective behaviors of a complex system emerge from the interactions among its basic units. Multiplex networks, i.e. networks with many layers,…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem…
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…
Network self-similarity or fractality are widely accepted as an important topological property of metabolic networks; however, recent studies cast doubt on the reality of self-similarity in the networks. Therefore, we perform a…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess…
Due to the complexity of the human body, most diseases present a high inter-personal variability in the way they manifest, i.e. in their phenotype, which has important clinical repercussions - as for instance the difficulty in defining…
Representation of cities as organisms with metabolic processes is a useful analogy for urban design, development and sustainability. Urban metabolism can be modeled by representing urban systems as networks. The various networks included in…
The study of complex networks has been historically based on simple graph data models representing relationships between individuals. However, often reality cannot be accurately captured by a flat graph model. This has led to the…
Recently, motivated by the pioneer works that reveal the small-world effect and scale-free property of various real-life networks, many scientists devote themselves into studying complex networks. One of the ultimate goals is to understand…
In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…
Identification of communities in complex networks has become an effective means to analysis of complex systems. It has broad applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
Networked structure emerged from a wide range of fields such as biological systems, World Wide Web and technological infrastructure. A deeply insight into the topological complexity of these networks has been gained. Some works start to pay…