Related papers: Rooted NNI moves on tree-based phylogenetic networ…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view…
Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply.…
We study the growth of a time-ordered rooted tree by probabilistic attachment of new vertices to leaves. We construct a likelihood function of the leaves based on the connectivity of the tree. We take such connectivity to be induced by the…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
In this article, we propose the approach to structural optimization of neural networks, based on the braid theory. The paper describes the basics of braid theory as applied to the description of graph structures of neural networks. It is…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Nested (or reconciled) phylogenetic trees model co-evolutionary systems in which one evolutionary history is embedded within another. We introduce a geometric framework for such systems by defining $\sigma$-space, a moduli space of fully…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
We analyze a class of spatial random spanning trees built on a realization of a homogeneous Poisson point process of the plane. This tree has a simple radial structure with the origin as its root. We first use stochastic geometry arguments…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
Nestedness is a common property of communication, finance, trade, and ecological networks. In networks with high levels of nestedness, the link positions of low-degree nodes (those with few links) form nested subsets of the link positions…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…