Related papers: On recognizing graphs representing Persistent Perf…
Tolerance graphs model interval relations in such a way that intervals can tolerate a certain degree of overlap without being in conflict. This subclass of perfect graphs has been extensively studied, due to both its interesting structure…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
A total dominating set in a graph is a set of vertices such that every vertex of the graph has a neighbor in the set. We introduce and study graphs that admit non-negative real weights associated to their vertices such that a set of…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were…
We present two deterministic dynamic algorithms for the maximum matching problem. (1) An algorithm that maintains a $(2+\epsilon)$-approximate maximum matching in general graphs with $O(\text{poly}(\log n, 1/\epsilon))$ update time. (2) An…
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…
Deciding whether a graph can be embedded in a grid using only unit-length edges is NP-complete, even when restricted to binary trees. However, it is not difficult to devise a number of graph classes for which the problem is polynomial, even…
The decision problem of perfect matchings in uniform hypergraphs is famously an NP-complete problem. It has been shown by Keevash--Knox--Mycroft [STOC, 2013] that for every $\varepsilon>0$, such decision problem restricted to $k$-uniform…
Haplotyping is the bioinformatics problem of predicting likely haplotypes based on given genotypes. It can be approached using Gusfield's perfect phylogeny haplotyping (PPH) method for which polynomial and linear time algorithms exist.…
Suppose we have a set $X$ consisting of $n$ taxa and we are given information from $k$ loci from which to construct a phylogeny for $X$. Each locus offers information for only a fraction of the taxa. The question is whether this data…
In the area of beyond-planar graphs, i.e. graphs that can be drawn with some local restrictions on the edge crossings, the recognition problem is prominent next to the density question for the different graph classes. For 1-planar graphs,…
Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also be useful for this task. Notably, perfect transfer networks (PTN) explain the character…
In a graph G, a dissociation set is a subset of vertices which induces a subgraph with vertex degree at most 1. Finding a dissociation set of maximum cardinality in a graph is NP-hard even for bipartite graphs and is called the maximum…
The maximum clique problem is a classical NP-complete problem in graph theory and has important applications in many domains. In this paper we show, in a partially non-constructive way, the existence of an exact polynomial-time algorithm…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
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…
It is well-known that the graph isomorphism problem can be posed as an equivalent problem of determining whether an auxiliary graph structure contains a clique of specific order. However, the algorithms that have been developed so far for…
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…