Related papers: Haplotype Inference for Pedigrees with Few Recombi…
Hypertree decompositions of hypergraphs are a generalization of tree decompositions of graphs. The corresponding hypertree-width is a measure for the cyclicity and therefore tractability of the encoded computation problem. Many NP-hard…
The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
We study homomorphism polynomials, which are polynomials that enumerate all homomorphisms from a pattern graph $H$ to $n$-vertex graphs. These polynomials have received a lot of attention recently for their crucial role in several new…
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…
Not all nodes in a network are created equal. Differences and similarities exist at both individual node and group levels. Disentangling single node from group properties is crucial for network modeling and structural inference. Based on…
We study the problem of determining the minimal genus of a simple finite connected graph. We present an algorithm which, for an arbitrary graph $G$ with $n$ vertices and $m$ edges, determines the orientable genus of $G$ in…
In recent years many algorithms have been developed for finding patterns in graphs and networks. A disadvantage of these algorithms is that they use subgraph isomorphism to determine the support of a graph pattern; subgraph isomorphism is a…
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…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
Pedigree polytopes are extensions of the classical Symmetric Traveling Salesman Problem polytopes whose graphs (1-skeletons) contain the TSP polytope graphs as spanning subgraphs. While deciding adjacency of vertices in TSP polytopes is…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
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.…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
Reconstruction of evolutionary relationships between species is an important topic in the field of computational biology. Pairwise compatibility graphs (PCGs) are used to model such relationships. A graph is a PCG if its edges can be…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
Recombination is a powerful evolutionary process that shapes the genetic diversity observed in the populations of many species. Reconstructing genealogies in the presence of recombination from sequencing data is a very challenging problem,…