Related papers: Behind Every Great Tree is a Great (Phylogenetic) …
A binary phylogenetic network on a taxon set $X$ is a rooted acyclic digraph in which the degree of each nonleaf node is three and its leaves (i.e.degree-one nodes) are uniquely labeled with the taxa of $X$. It is tree-child if each nonleaf…
Many systems in nature, society and technology can be described as networks, where the vertices are the system's elements and edges between vertices indicate the interactions between the corresponding elements. Edges may be weighted if the…
We introduce a growing network model in which a new node attaches to a randomly-selected node, as well as to all ancestors of the target node. This mechanism produces a sparse, ultra-small network where the average node degree grows…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
We prove that every connected graph with $s$ vertices of degree not 2 has a spanning tree with at least ${1\over 4}(s-2)+2$ leaves. Let $G$ be a be a connected graph of girth $g$ with $v>1$ vertices. Let maximal chain of successively…
Real networks exhibit nontrivial topological features such as heavy-tailed degree distribution, high clustering, and small-worldness. Researchers have developed several generative models for synthesizing artificial networks that are…
A circle graph is an intersection graph of a set of chords of a circle. We describe the unavoidable induced subgraphs of circle graphs with large treewidth. This includes examples that are far from the `usual suspects'. Our results imply…
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree…
We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is…
Brain networks exhibit remarkable structural properties, including high local clustering, short path lengths, and heavy-tailed weight and degree distributions. While these features are thought to enable efficient information processing with…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
Geometry of networks endowed with a causal structure is discussed using the conventional framework of equilibrium statistical mechanics. The popular growing network models appear as particular causal models. We focus on a class of tree…
For a graph $G$, an edge-separating (resp. vertex-separating) path system of $G$ is a family of paths in $G$ such that for any pair of edges $e_1, e_2$ (resp. pair of vertices $v_1, v_2$) of $G$ there is at least one path in the family that…
A common task in phylogenetics is to find an evolutionary tree representing proximity relationships between species. This motivates the notion of leaf powers: a graph G = (V, E) is a leaf power if there exist a tree T on leafset V and a…
Metric graph properties lie in the heart of the analysis of complex networks, while in this paper we study their convexity through mathematical definition of a convex subgraph. A subgraph is convex if every geodesic path between the nodes…
Models of growing networks are a central topic in network science. In these models, vertices are usually labeled by their arrival time, distinguishing even those node pairs whose structural roles are identical. In contrast, unlabeled…
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,…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
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…