Related papers: Identifying circular orders for blobs in phylogene…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We…

Our interest is in multiplex network data with multiple network samples observed across the same set of nodes. Examples originate from a variety of fields, including brain connectivity, international trade networks, and social networks,…

Recently, there has been a growing interest in the relationships between unrooted and rooted phylogenetic networks. In this context, a natural question to ask is if an unrooted phylogenetic network U can be oriented as a rooted phylogenetic…

Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…

Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…

Links in a practical network may have different functions, which makes the original network a combination of some functional subnetworks. Here, by a model of coupled oscillators, we investigate how such functional subnetworks are evolved…

Higher order networks are able to characterize data as different as functional brain networks, protein interaction networks and social networks beyond the framework of pairwise interactions. Most notably higher order networks include…

Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…

A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…

The social networks that infectious diseases spread along are typically clustered. Because of the close relation between percolation and epidemic spread, the behavior of percolation in such networks gives insight into infectious disease…

Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…

Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…

Network classification aims to group networks (or graphs) into distinct categories based on their structure. We study the connection between classification of a network and of its constituent nodes, and whether nodes from networks in…

Complex networks are a powerful modeling tool, allowing the study of countless real-world systems. They have been used in very different domains such as computer science, biology, sociology, management, etc. Authors have been trying to…

We study complex networks in which the nodes of the network are tagged with different colors depending on the functionality of the nodes (colored graphs), using information theory applied to the distribution of motifs in such networks. We…

Network science has presented community detection as a valuable tool for revealing functional modules in complex systems rooted in the wiring architectures of complex networks. The varying procedures of community detection can produce,…

Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of…

Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…