11 citations · 23 across the 30 of their papers we have counts for
30 papers
A characterization of terminal planar networks by forbidden structures
Haruki Miyaji, Yuki Noguchi, Hexuan Liu +4
The class of terminal planar networks was recently introduced from a biological perspective in relation to the visualization of phylogenetic networks, and its connection to upward…
Asymptotic Enumeration of Subclasses of Level- Phylogenetic Networks
Hexuan Liu, Bing-Ze Lu, Taoyang Wu +1
This paper studies the enumeration of seven subclasses of level- phylogenetic networks under various planarity and structural constraints, including terminal planar, tree-child,…
SPRINT: A fast, new software tool for reconstructing the evolutionary past of polyploid datasets
Liam J. Maher, Taoyang Wu, Katharina T. Huber
Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploid…
Planar Rooted Phylogenetic Networks
Vincent Moulton, Taoyang Wu
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution…
Distributions of cherries and pitchforks for the Ford model
Gursharn Kaur, Kwok Pui Choi, Taoyang Wu
We study two fringe subtree counting statistics, the number of cherries and that of pitchforks for Ford's model, a one-parameter family of random phylogenetic tree models that…
Encoding and ordering X-cactuses
Andrew Francis, Katharina T. Huber, Vincent Moulton +1
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A specia…
On asymptotic joint distributions of cherries and pitchforks for random phylogenetic trees
Kwok Pui Choi, Gursharn Kaur, Taoyang Wu
Tree shape statistics provide valuable quantitative insights into evolutionary mechanisms underpinning phylogenetic trees, a commonly used graph representation of evolution systems…
On cherry and pitchfork distributions of random rooted and unrooted phylogenetic trees
Kwok Pui Choi, Ariadne Thompson, Taoyang Wu
Tree shape statistics are important for investigating evolutionary mechanisms mediating phylogenetic trees. As a step towards bridging shape statistics between rooted and unrooted…
Treewidth of display graphs: bounds, brambles and applications
Remie Janssen, Mark Jones, Steven Kelk +2
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or…
Quarnet inference rules for level-1 networks
Katharine T. Huber, Vincent Moulton, Charles Semple +1
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic…
UPGMA and the normalized equidistant minimum evolution problem
Vincent Moulton, Andreas Spillner, Taoyang Wu
UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum e…
Treewidth distance on phylogenetic trees
Steven Kelk, Georgios Stamoulis, Taoyang Wu
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves…
A cubic-time algorithm for computing the trinet distance between level-1 networks
Vincent Moulton, James Oldman, Taoyang Wu
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination…
Bounds for phylogenetic network space metrics
Andrew Francis, Katharina Huber, Vincent Moulton +1
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was intr…
Binets: fundamental building blocks for phylogenetic networks
Leo van Iersel, Vincent Moulton, Eveline de Swart +1
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Esse…
Transforming phylogenetic networks: Moving beyond tree space
Katharina T. Huber, Vincent Moulton, Taoyang Wu
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networ…
Reduction rules for the maximum parsimony distance on phylogenetic trees
Steven Kelk, Mareike Fischer, Vincent Moulton +1
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions o…
On joint subtree distributions under two evolutionary models
Taoyang Wu, Kwok Pui Choi
In population and evolutionary biology, hypotheses about micro-evolutionary and macro-evolutionary processes are commonly tested by comparing the shape indices of empirical evoluti…
Folding and unfolding phylogenetic trees and networks
Katharina T. Huber, Vincent Moulton, Mike Steel +1
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic net…
Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets
Katharina Huber, Leo van Iersel, Vincent Moulton +2
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network…
Clades and clans: a comparison study of two evolutionary models
Sha Zhu, Cuong Than, Taoyang Wu
The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary bio…
Representing Partitions on Trees
Katharina T. Huber, Vincent Moulton, Charles Semple +1
In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set of species from a multiset of partitions corresponding to various at…
The Combinatorics of Tandem Duplication
L Penso-Dolfin, CD Greenman
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give ris…
Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History
Si Li, Kwok Pui Choi, Taoyang Wu +1
Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapsho…