相关论文: Clustering Systems of Phylogenetic Networks

Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…

Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small…

Transport networks are crucial to the functioning of natural systems and technological infrastructures. For flow networks in many scenarios, such as rivers or blood vessels, acyclic networks (i.e., trees) are optimal structures when…

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…

Reputation-based cooperation on social networks offers a causal mechanism between graph properties and social trust. Recent papers on the `structural microfoundations` of the society used this insight to show how demographic processes, such…

Clustering, assortativity, and communities are key features of complex networks. We probe dependencies between these attributes and find that ensembles with strong clustering display both high assortativity by degree and prominent community…

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…

Clustering is a fundamental property of complex networks and it is the mathematical expression of a ubiquitous phenomenon that arises in various types of self-organized networks such as biological networks, computer networks or social…

Percolation theory can be used to describe the structural properties of complex networks using the generating function formulation. This mapping assumes that the network is locally tree-like and does not contain short-range loops between…

Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…

Triadic closure, the formation of a connection between two nodes in a network sharing a common neighbor, is considered a fundamental mechanism determining the clustered nature of many real-world topologies. In this work we define a static…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…

Community detection, which focuses on clustering nodes or detecting communities in (mostly) a single network, is a problem of considerable practical interest and has received a great deal of attention in the research community. While being…

Rooted binary phylogenetic networks are extensions of rooted binary trees, adding reticulation nodes that are designed to represent evolutionary processes that involve hybridization events. Enumerative combinatorics studies have counted…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. The second…

Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…