Related papers: Complexity of Modification Problems for Reciprocal…
Best match graphs (BMGs) are vertex-colored directed graphs that were introduced to model the relationships of genes (vertices) from different species (colors) given an underlying evolutionary tree that is assumed to be unknown. In…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
Quasi-best match graphs (qBMGs) are a hereditary class of directed, properly vertex-colored graphs. They arise naturally in mathematical phylogenetics as a generalization of best match graphs, which formalize the notion of evolutionary…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
Can we efficiently compute optimal solutions to instances of a hard problem from optimal solutions to neighboring (i.e., locally modified) instances? For example, can we efficiently compute an optimal coloring for a graph from optimal…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…
Graph matching, also known as network alignment, refers to finding a bijection between the vertex sets of two given graphs so as to maximally align their edges. This fundamental computational problem arises frequently in multiple fields…
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 $G$?…
The paper considers the NP-hard graph vertex coloring problem, which differs from traditional problems in which it is required to color vertices with a given (or minimal) number of colors so that adjacent vertices have different colors. In…
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…
We contribute to the theoretical understanding of randomized search heuristics for dynamic problems. We consider the classical vertex coloring problem on graphs and investigate the dynamic setting where edges are added to the current graph.…
We study weighted edge coloring of graphs, where we are given an undirected edge-weighted general multi-graph $G := (V, E)$ with weights $w : E \rightarrow [0, 1]$. The goal is to find a proper weighted coloring of the edges with as few…
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…
Ordered matchings, defined as graphs with linearly ordered vertices, where each vertex is connected to exactly one edge, play a crucial role in the area of ordered graphs and their homomorphisms. Therefore, we consider related problems from…
In this paper we consider a variation of a recoloring problem, called the Color-Fixing. Let us have some non-proper $r$-coloring $\varphi$ of a graph $G$. We investigate the problem of finding a proper $r$-coloring of $G$, which is "the…