Related papers: Maximizing Phylogenetic Diversity under Ecological…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
In the problem Fault-Tolerant Path (FTP), we are given an edge-weighted directed graph G = (V, E), a subset U \subseteq E of vulnerable edges, two vertices s, t \in V, and integers k and \ell. The task is to decide whether there exists a…
'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…
We introduce and study the complexity of Path Packing. Given a graph $G$ and a list of paths, the task is to embed the paths edge-disjoint in $G$. This generalizes the well known Hamiltonian-Path problem. Since Hamiltonian Path is…
The online dominating set problem is an online variant of the minimum dominating set problem, which is one of the most important NP-hard problems on graphs. This problem is defined as follows: Given an undirected graph $G = (V, E)$, in…
In the NP-hard Edge Dominating Set problem (EDS) we are given a graph $G=(V,E)$ and an integer $k$, and need to determine whether there is a set $F\subseteq E$ of at most $k$ edges that are incident with all (other) edges of $G$. It is…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
The maximum modularity of a graph is a parameter widely used to describe the level of clustering or community structure in a network. Determining the maximum modularity of a graph is known to be NP-complete in general, and in practice a…
This paper introduces the \emph{$d$-distance matching problem}, in which we are given a bipartite graph $G=(S,T;E)$ with $S=\{s_1,\dots,s_n\}$, a weight function on the edges and an integer $d\in\mathbb Z_+$. The goal is to find a maximum…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
The question what determines the structure of natural food webs has been listed among the nine most important unanswered questions in ecology. It arises naturally from many problems related to ecosystem stability and resilience. The…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…
Given a graph $G$ and an integer $b$, Bandwidth asks whether there exists a bijection $\pi$ from $V(G)$ to $\{1, \ldots, |V(G)|\}$ such that $\max_{\{u, v \} \in E(G)} | \pi(u) - \pi(v) | \leq b$. This is a classical NP-complete problem,…
Deletion problems are those where given a graph $G$ and a graph property $\pi$, the goal is to find a subset of edges such that after its removal the graph $G$ will satisfy the property $\pi$. Typically, we want to minimize the number of…
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…
An out-tree $T$ of a directed graph $D$ is a rooted tree subgraph with all arcs directed outwards from the root. An out-branching is a spanning out-tree. By $l(D)$ and $l_s(D)$ we denote the maximum number of leaves over all out-trees and…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…