Related papers: Maximizing Phylogenetic Diversity under Ecological…
For many taxa, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…
Grid graphs, and, more generally, $k\times r$ grid graphs, form one of the most basic classes of geometric graphs. Over the past few decades, a large body of works studied the (in)tractability of various computational problems on grid…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
A set S of vertices of a graph is a defensive alliance if, for each element of S, the majority of its neighbors is in S. The problem of finding a defensive alliance of minimum size in a given graph is NP-hard and there are polynomial-time…
A set $S$ of vertices of a graph is a defensive alliance if, for each element of $S$, the majority of its neighbours is in $S$. We consider the notion of local minimality in this paper. We are interested in locally minimal defensive…
In Path Set Packing, the input is an undirected graph $G$, a collection $\calp$ of simple paths in $G$, and a positive integer $k$. The problem is to decide whether there exist $k$ edge-disjoint paths in $\calp$. We study the parameterized…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…
We study the problem Symmetric Directed Multicut from a parameterized complexity perspective. In this problem, the input is a digraph $D$, a set of cut requests $C=\{(s_1,t_1),\ldots,(s_\ell,t_\ell)\}$ and an integer $k$, and the task is to…
The Edge Multicut problem is a classical cut problem where given an undirected graph $G$, a set of pairs of vertices $\mathcal{P}$, and a budget $k$, the goal is to determine if there is a set $S$ of at most $k$ edges such that for each…
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 study the Steiner Tree problem on unit disk graphs. Given a $n$ vertex unit disk graph $G$, a subset $R\subseteq V(G)$ of $t$ vertices and a positive integer $k$, the objective is to decide if there exists a tree $T$ in $G$ that spans…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
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…
A complexity-theoretic approach to studying biological networks is proposed. A simple graph representation is used where molecules (DNA, RNA, proteins and chemicals) are vertices and relations between them are directed and signed…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Given a graph $G=(V,E)$, a set $\mathcal{F}$ of forbidden subgraphs, we study $\mathcal{F}$-Free Edge Deletion, where the goal is to remove minimum number of edges such that the resulting graph does not contain any $F\in \mathcal{F}$ as a…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…