Related papers: Regular networks are determined by their trees
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
We introduce the concept of community trees that summarizes topological structures within a network. A community tree is a tree structure representing clique communities from the clique percolation method (CPM). The community tree also…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
The graph reconstruction conjecture states that all graphs on at least three vertices are determined up to isomorphism by their deck. In this paper, a general framework for this problem is proposed to simply explain the reconstruction of…
Any graph which is not vertex transitive has a proper induced subgraph which is unique due to its structure or the way of its connection to the rest of the graph. We have called such subgraph as an anchor. Using an anchor which, in fact, is…
A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
The recursive removal of leaves (dead end vertices) and their neighbors from an undirected network results, when this pruning algorithm stops, in a so-called core of the network. This specific subgraph should be distinguished from…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
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}…
Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…
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…
Let $G$ be a graph with $n$ vertices, and let $A(G)$ and $D(G)$ denote respectively the adjacency matrix and the degree matrix of $G$. Define $$ A_{\alpha}(G)=\alpha D(G)+(1-\alpha)A(G) $$ for any real $\alpha\in [0,1]$. The collection of…
Graphs are called navigable if one can find short paths through them using only local knowledge. It has been shown that for a graph to be navigable, its construction needs to meet strict criteria. Since such graphs nevertheless seem to…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
For a given graph, the unlabeled subgraphs $G-v$ are called the cards of $G$ and the deck of $G$ is the multiset $\{G-v: v \in V(G)\}$. Wendy Myrvold [Ars Combinatoria, 1989] showed that a non-connected graph and a connected graph both on…
Network motifs are characteristic patterns which occur in the networks essentially more frequently than the other patterns. For five motifs found in S. Itzkovitz, U. Alon, Phys. Rev.~E, 2005, 71, 026117-1, hierarchical random graphs are…
The transmission of a vertex $v$ of a graph $G$ is the sum of distances from $v$ to all the other vertices in $G$. A graph is transmission irregular if all of its vertices have pairwise different transmissions. A starlike tree…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…