Related papers: Behind Every Great Tree is a Great (Phylogenetic) …
We introduce a new family of models for growing networks. In these networks new edges are attached preferentially to vertices with higher number of connections, and new vertices are created by already existing ones, inheriting part of their…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
We prove that, if $m$ is sufficiently large, every graph on $m+1$ vertices that has a universal vertex and minimum degree at least $\lfloor \frac{2m}{3} \rfloor$ contains each tree $T$ with $m$ edges as a subgraph. Our result confirms, for…
Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply.…
A spanning tree $T$ of a connected graph $G$ is a subgraph of $G$ that is a tree covers all vertices of $G$. The leaf distance of $T$ is defined as the minimum of distances between any two leaves of $T$. A fractional matching of a graph $G$…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
In networks that grow by isotropic redirection (IR), a new node selects an initial target node uniformly at random and attaches to a randomly chosen neighbor of the target. The emerging networks exhibit leaf proliferation, in which the…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
This work explores hypernetworks: an approach of using a one network, also known as a hypernetwork, to generate the weights for another network. Hypernetworks provide an abstraction that is similar to what is found in nature: the…
A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
We give exact relations for certain types of the hierarchic fractal structures. In the blatant distinction from regular networks of the "small world" (SW) topology [1], regular fractal networks manifests the logarithmic dependence of the…
In this paper it is shown that for any network there is a uniquely determined network based on a structure tree that provides a convenient way of determining a minimal cut separating a pair $s, t$ where each of $s, t$ is either a vertex or…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…