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We introduce and investigate the approximability of the maximum binary tree problem (MBT) in directed and undirected graphs. The goal in MBT is to find a maximum-sized binary tree in a given graph. MBT is a natural variant of the…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a spanning tree in which any two adjacent edges have distinct colors. Since finding such a tree is NP-hard in general,…
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…
In a bounded max-coloring of a vertex/edge weighted graph, each color class is of cardinality at most $b$ and of weight equal to the weight of the heaviest vertex/edge in this class. The bounded max-vertex/edge-coloring problems ask for…
A rainbow matching in an edge-colored graph is a matching whose edges have distinct colors. We address the complexity issue of the following problem, \mrbm: Given an edge-colored graph $G$, how large is the largest rainbow matching in $G$?…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures 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…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
In the Maximum-size Properly Colored Forest problem, we are given an edge-colored undirected graph and the goal is to find a properly colored forest with as many edges as possible. We study this problem within a broader framework by…
For a set $R$ of $n$ red points and a set $B$ of $n$ blue points, a $BR$-matching is a non-crossing geometric perfect matching where each segment has one endpoint in $B$ and one in $R$. Two $BR$-matchings are compatible if their union is…
The quest for colorful components (connected components where each color is associated with at most one vertex) inside a vertex-colored graph has been widely considered in the last ten years. Here we consider two variants, Minimum Colorful…
A vertex of a plane digraph is bimodal if all its incoming edges (and hence all its outgoing edges) are consecutive in the cyclic order around it. A plane digraph is bimodal if all its vertices are bimodal. Bimodality is at the heart of…
A graph G is called well-indumatched if all of its maximal induced matchings have the same size. In this paper we characterize all well-indumatched trees. We provide a linear time algorithm to decide if a tree is well-indumatched or not.…
Fitch graphs $G=(X,E)$ are digraphs that are explained by $\{\emptyset, 1\}$-edge-labeled rooted trees $T$ with leaf set $X$: there is an arc $(x,y) \in E$ if and only if the unique path in $T$ that connects the last common ancestor…
Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurovi\'c et al. (IEEE TCBB, to appear) introduced the minimum conflict-free row split (MCRS) problem: split each row of a…
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…
The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a…