Related papers: Generalized Fitch Graphs: Edge-labeled Graphs that…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of…
In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Pairwise compatibility graphs (PCGs) with non-negative integer edge weights recently have been used to describe rare evolutionary events and scenarios with horizontal gene transfer. Here we consider the case that vertices are separated by…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
The modular decomposition of a graph $G$ is a natural construction to capture key features of $G$ in terms of a labeled tree $(T,t)$ whose vertices are labeled as "series" ($1$), "parallel" ($0$) or "prime". However, full information of $G$…
In this paper, we propose a new type of graph, denoted as "embedded-graph", and its theory, which employs a distributed representation to describe the relations on the graph edges. Embedded-graphs can express linguistic and complicated…
Let $G(V, E)$ be a simple connected graph, with $|E| = \epsilon.$ In this paper, we define an edge-set graph $\mathcal G_G$ constructed from the graph $G$ such that any vertex $v_{s,i}$ of $\mathcal G_G$ corresponds to the $i$-th…
Extremal graph theory studies the maximum or minimum number of subgraphs isomorphic to a prescribed graph under given constraints. \textit{Localization} has recently emerged as a framework that refines such problems by assigning extremal…
Given a finite group $G$ and its representation $\rho$, the corresponding McKay graph is a graph $\Gamma(G,\rho)$ whose vertices are the irreducible representations of $G$; the number of edges between two vertices $\pi,\tau$ of…
A graph $G$ is a pairwise compatibility graph (PCG) if there exists an edge-weighted tree and an interval $I$, such that each leaf of the tree is a vertex of the graph, and there is an edge $\{ x, y \}$ in $G$ if and only if the weight of…
A digraph is connected-homogeneous if any isomorphism between finite connected induced subdigraphs extends to an automorphism of the digraph. We consider locally-finite connected-homogeneous digraphs with more than one end. In the case that…
A tree with at most k leaves is called k-ended tree, and a tree with exactly k leaves is called k-end tree, where a leaf is a vertex of degree one. Contraction of a graph G along the edge e means deleting the edge e and identifying its end…
Several implicit methods to infer Horizontal Gene Transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the…
Let G be a graph whose edges are labeled by ideals of a commutative ring. We introduce a generalized spline, which is a vertex-labeling of G by elements of the ring so that the difference between the labels of any two adjacent vertices lies…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Bispanning graphs are undirected graphs with an edge set that can be decomposed into two disjoint spanning trees. The operation of symmetrically swapping two edges between the trees, such that the result is a different pair of disjoint…
Arboreal networks are a generalization of rooted trees, defined by keeping the tree-like structure, but dropping the requirement for a single root. Just as the class of cographs is precisely the class of undirected graphs that can be…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…