Related papers: Checking Phylogenetic Decisiveness in Theory and i…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
The roles played by decision factors in making complex subject are decisions are characterized by how these factors affect the overall decision. Evidence that partially matches a factor is evaluated, and then effective computational rules…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
The paper is devoted to the study of combinatorial determinacy properties of a family of substitution complexes consisting of quadrilaterals glued side-to-side with each other. These properties are useful in constructing algebraic…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…
Studies of the genetic loci that contribute to variation in gene expression frequently identify loci with broad effect on gene expression: expression quantitative trait locus (eQTL) hotspots. We describe a set of exploratory graphical…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
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…
We consider the algorithmic decision problem that takes as input an $n$-vertex $k$-uniform hypergraph $H$ with minimum codegree at least $m-c$ and decides whether it has a matching of size $m$. We show that this decision problem is fixed…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
A quick proof of Gallai's celebrated theorem on color-critical graphs is given from Gallai's simple, ingenious lemma on factor-critical graphs, in terms of partitioning the vertex-set into a minimum number of hyperedges of a hereditary…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
We study the problem of bi-chromatic coloring of hypergraphs in the LOCAL distributed model of computation. This problem can easily be solved by a randomized local algorithm with no communication. However, it is not known how to solve it…
The computation of short paths in graphs with arc lengths is a pillar of graph algorithmics and network science. In a more diverse world, however, not every short path is equally valuable. For the setting where each vertex is assigned to a…
We discuss proving correctness and completeness of definite clause logic programs. We propose a method for proving completeness, while for proving correctness we employ a method which should be well known but is often neglected. Also, we…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
We provide a constraint based computational model of linear precedence as employed in the HPSG grammar formalism. An extended feature logic which adds a wide range of constraints involving precedence is described. A sound, complete and…