Related papers: Visualizing Geophylogenies -- Internal and Externa…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
In this paper we look at the problem of adjacency labeling of graphs. Given a family of undirected graphs the problem is to determine an encoding-decoding scheme for each member of the family such that we can decode the adjacency…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
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…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
While deep learning has revolutionized the prediction of rigid protein structures, modelling the conformational ensembles of Intrinsically Disordered Proteins (IDPs) remains a key frontier. Current AI paradigms present a trade-off: Protein…
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…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
In 1989 Erd\H{o}s and Sz\'ekely showed that there is a bijection between (i) the set of rooted trees with $n+1$ vertices whose leaves are bijectively labeled with the elements of $[\ell]=\{1,2,\dots,\ell\}$ for some $\ell \leq n$, and (ii)…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…
We introduce an approach for updating older tree inventories with geographic coordinates using street-level panorama images and a global optimization framework for tree instance matching. Geolocations of trees in inventories until the early…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
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…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
A witness drawing of a graph is a visualization that clearly shows a given property of a graph. We study and implement various drawing paradigms for witness drawings to clearly show that graphs have bounded pathwidth or treewidth. Our…