5 citations · 10 across the 9 of their papers we have counts for
11 papers
Combinatorial and computational investigations of Neighbor-Joining bias
Ruth Davidson, Abraham Martin del Campo
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimil…
RGB image-based data analysis via discrete Morse theory and persistent homology
Chuan Du, Christopher Szul, Adarsh Manawa +3
Understanding and comparing images for the purposes of data analysis is currently a very computationally demanding task. A group at Australian National University (ANU) recently de…
Dimensions of Group-based Phylogenetic Mixtures
Hector Baños, Nathaniel Bushek, Ruth Davidson +6
In this paper we study group-based Markov models of evolution and their mixtures. In the algebreo-geometric setting, group-based phylogenetic tree models correspond to toric variet…
A combinatorial method for connecting BHV spaces representing different numbers of taxa
Yingying Ren, Sihan Zha, Jingwen Bi +5
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geod…
Phylogenetic trees
Hector Baños, Nathaniel Bushek, Ruth Davidson +6
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information o…
Modeling the distribution of distance data in Euclidean space
Ruth Davidson, Joseph Rusinko, Zoe Vernon +1
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, compu…
Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods
Ruth Davidson, MaLyn Lawhorn, Joseph Rusinko +1
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all d…
A new shellability proof of an identity of Dixon
Ruth Davidson, Augustine O'Keefe, Daniel Parry
We give a new proof of an old identity of Dixon (1865-1936) that uses tools from topological combinatorics. Dixon's identity is re-established by constructing an infinite family of…
Distance-based phylogenetic methods around a polytomy
Ruth Davidson, Seth Sullivant
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree…
Polyhedral Combinatorics of UPGMA Cones
Ruth Davidson, Seth Sullivant
Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatori…
A lexicographic shellability characterization of geometric lattices
Ruth Davidson, Patricia Hersh
Geometric lattices are characterized in this paper as those finite, atomic lattices such that every atom ordering induces a lexicographic shelling given by an edge labeling known a…