Related papers: Behind Every Great Tree is a Great (Phylogenetic) …
Many real life networks present an average path length logarithmic with the number of nodes and a degree distribution which follows a power law. Often these networks have also a modular and self-similar structure and, in some cases -…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
We present a link-by-link rule-based method for constructing all members of the ensemble of spanning trees for any recursively generated, finitely articulated graph, such as the DGM net. The recursions allow for many large-scale properties…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
We introduce the concept of Most, and Least, Compact Spanning Trees - denoted respectively by $T^*(G)$ and $T^\#(G)$ - of a simple, connected, undirected and unweighted graph $G(V, E, W)$. For a spanning tree $T(G) \in \mathcal{T}(G)$ to be…
Hierarchical tree structures are common in many real-world systems, from tree roots and branches to neuronal dendrites and biologically inspired artificial neural networks, as well as in technological networks for organizing and searching…
The minimal number of rooted subtree prune and regraft (rSPR) operations needed to transform one phylogenetic tree into another one induces a metric on phylogenetic trees - the rSPR-distance. The rSPR-distance between two phylogenetic trees…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
The Minimum Branch Vertices Spanning Tree problem aims to find a spanning tree $T$ in a given graph $G$ with the fewest branch vertices, defined as vertices with a degree three or more in $T$. This problem, known to be NP-hard, has…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
Routing information through networks is a universal phenomenon in both natural and manmade complex systems. When each node has full knowledge of the global network connectivity, finding short communication paths is merely a matter of…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Two new classes of networks are introduced that resemble small-world properties. These networks are recursively constructed but retain a fixed, regular degree. They consist of a one-dimensional lattice backbone overlayed by a hierarchical…
Many innovations are inspired by past ideas in a non-trivial way. Tracing these origins and identifying scientific branches is crucial for research inspirations. In this paper, we use citation relations to identify the descendant chart,…
We introduce the problem of finding a spanning tree along with a partition of the tree edges into fewest number of feasible sets, where constraints on the edges define feasibility. The motivation comes from wireless networking, where we…
Let $k$, $d$ be a positive integer, $G$ be a connected graph of order $n$, $T$ be a tree. The leaf distance of a tree is defined as the minimum distance between any two leaves. For $v\in V(T)$, the leaf degree of $v$ in $T$ is the number of…
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…
Inspired by studies on the airports' network and the physical Internet, we propose a general model of weighted networks via an optimization principle. The topology of the optimal network turns out to be a spanning tree that minimizes a…