Related papers: Circular Networks from Distorted Metrics
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
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…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
A new method for identifying communities in networks is proposed. Reference nodes, either selected using a priory information about the network or according to relevant node measurements, are obtained so as to indicate putative communities.…
We introduce the concept of Random Sequential Renormalization (RSR) for arbitrary networks. RSR is a graph renormalization procedure that locally aggregates nodes to produce a coarse grained network. It is analogous to the (quasi-)parallel…
Much of contemporary systems biology owes its success to the abstraction of a network, the idea that diverse kinds of molecular, cellular, and organismal species and interactions can be modeled as relational nodes and edges in a graph of…
Network science is a rapidly expanding field, with a large and growing body of work on network-based dynamical processes. Most theoretical results in this area rely on the so-called \emph{locally tree-like approximation}. This is, however,…
The application of the network approach to the urban case poses several questions in terms of how to deal with metric distances, what kind of graph representation to use, what kind of measures to investigate, how to deepen the correlation…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for {\it bicombining tree-child networks}…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
A rooted acyclic digraph N with labelled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general,…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
The stability and ability of an ecosystem to withstand climate change is directly linked to its biodiversity. Dead trees are a key indicator of overall forest health, housing one-third of forest ecosystem biodiversity, and constitute 8%of…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication networks, as well as systems constrained in…
Clustering is the propensity of nodes that share a common neighbour to be connected. It is ubiquitous in many networks but poses many modelling challenges. Clustering typically manifests itself by a higher than expected frequency of…