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The study of triangles in graphs is a standard tool in network analysis, leading to measures such as the \emph{transitivity}, i.e., the fraction of paths of length $2$ that participate in triangles. Real-world networks are often directed,…
Interconnected networks describe the dynamics of important systems in a wide range such as biological systems and electrical power grids. Some important features of these systems were successfully studied and understood through simplified…
Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…
The study of how diseases spread has greatly benefited from advances in network modeling. Recently, a class of networks known as multilayer graphs has been shown to describe more accurately many real systems, making it possible to address…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…
The contact structure between hosts has a critical influence on disease spread. However, most networkbased models used in epidemiology tend to ignore heterogeneity in the weighting of contacts. This assumption is known to be at odds with…
In order to take the weight of connection into consideration and to find a natural measurement of weight, we have collected papers in Econophysics and constructed a network of scientific communication to integrate idea transportation among…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
The graphical notion of effective resistance has found wide-ranging applications in many areas of pure mathematics, applied mathematics and control theory. By the nature of its construction, effective resistance can only be computed in…
We propose a novel approach to the estimation of multiple Graphical Models to analyse temporal patterns of association among a set of metabolites over different groups of patients. Our motivating application is the Southall And Brent…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
The relation between network structure and dynamics is determinant for the behavior of complex systems in numerous domains. An important long-standing problem concerns the properties of the networks that optimize the dynamics with respect…
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…
One of the most important challenges in network science is to quantify the information encoded in complex network structures. Disentangling randomness from organizational principles is even more demanding when networks have a multiplex…
Graph neural networks can accurately predict the chemical properties of many molecular systems, but their suitability for large, macromolecular assemblies such as gels is unknown. Here, graph neural networks were trained and optimised for…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
While operating communication networks adaptively may improve utilization and performance, frequent adjustments also introduce an algorithmic challenge: the re-optimization of traffic engineering solutions is time-consuming and may limit…