Related papers: Algorithms for the Constrained Perfect Phylogeny w…
In a graph, a perfect matching cut is an edge cut that is a perfect matching. Perfect Matching Cut (PMC) is the problem of deciding whether a given graph has a perfect matching cut, and is known to be NP-complete. We revisit the problem and…
Motivated by problems of comparative genomics and paleogenomics, in [Chauve et al., 2009], the authors introduced the Gapped Consecutive-Ones Property Problem (k,delta)-C1P: given a binary matrix M and two integers k and delta, can the…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Constraint Satisfaction Problem on finite sets is known to be NP-complete in general but certain restrictions on the constraint language can ensure tractability. It was proved that if a constraint language has a weak near unanimity…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Parameterized complexity theory has enabled a refined classification of the difficulty of NP-hard optimization problems on graphs with respect to key structural properties, and so to a better understanding of their true difficulties. More…
Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
Determinantal Point Processes (DPPs) are probabilistic models that arise in quantum physics and random matrix theory and have recently found numerous applications in computer science. DPPs define distributions over subsets of a given ground…
We call change-point problem (CPP) the identification of changes in the probabilistic behavior of a sequence of observations. Solving the CPP involves detecting the number and position of such changes. In genetics the study of how and what…
Permutation Pattern Matching (PPM) is the problem of deciding for a given pair of permutations P and T whether the pattern P is contained in the text T. Bose, Buss and Lubiw showed that PPM is NP-complete. In view of this result, it is…
Finding complete subgraphs in a graph, that is, cliques, is a key problem and has many real-world applications, e.g., finding communities in social networks, clustering gene expression data, modeling ecological niches in food webs, and…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
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…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
We continue and extend previous work on the parameterized complexity analysis of the NP-hard Stable Roommates with Ties and Incomplete Lists problem, thereby strengthening earlier results both on the side of parameterized hardness as well…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…