相关论文: Combinatorics of pedigrees

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…

There is a unique path from the root of a tree to any other vertex. Every vertex, except the root, has a parent: the adjoining vertex on this unique path. This is the conventional definition of the parent vertex. For complete binary trees,…

In enumerative combinatorics, it is often a goal to enumerate both labeled and unlabeled structures of a given type. The theory of combinatorial species is a novel toolset which provides a rigorous foundation for dealing with the…

Traditionally, reconfiguration problems ask the question whether a given solution of an optimization problem can be transformed to a target solution in a sequence of small steps that preserve feasibility of the intermediate solutions. In…

We consider the classical problems (Edge) Steiner Tree and Vertex Steiner Tree after restricting the input to some class of graphs characterized by a small set of forbidden induced subgraphs. We show a dichotomy for the former problem…

Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no…

We consider upward-planar layered drawings of directed graphs, i.e., crossing-free drawings in which each edge is drawn as a y-monotone curve going upward from its tail to its head, and the y-coordinates of the vertices are integers. The…

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…

We describe a graph reduction operation, generalizing three graph reduction operations related to gene assembly in ciliates. The graph formalization of gene assembly considers three reduction rules, called the positive rule, double rule,…

We begin a systematic study of the enumerative combinatorics of mixed succession rules, which are succession rules such that, in the associated generating tree, the nodes are allowed to produce their sons at several different levels…

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…

Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…

The family of graphs that can be constructed from isolated vertices by disjoint union and graph join operations are called cographs. These graphs can be represented in a tree-like representation termed parse tree or cotree. In this paper,…

A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life.' In this paper we use an…

A class $\mathcal{G}$ of graphs is called hereditary if it is closed under taking induced subgraphs. We denote by $G^{epex}$ the class of graphs that are at most one edge away from being in $\mathcal{G}$. We note that $G^{epex}$ is…

We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…

An ordered graph is a graph together with a linear order on its vertices. A hereditary property of ordered graphs is a collection of ordered graphs closed under taking induced ordered subgraphs. If P is a property of ordered graphs, then…

Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…

Index structures are a building block of query processing and computer science in general. Since the dawn of computer technology there have been index structures. And since then, a myriad of index structures are being invented and published…

Threshold graphs are recursive deterministic network models that have been proposed for describing certain economic and social interactions. One drawback of this graph family is that it has limited generative attachment rules. To mitigate…