Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial
Phylogenetic trees are a central tool in many areas of life science and medicine. They
demonstrate evolutionary patterns among species, genes, and patterns of ancestry among …
demonstrate evolutionary patterns among species, genes, and patterns of ancestry among …
Comparing the topology of phylogenetic network generators
Phylogenetic networks represent evolutionary history of species and can record natural
reticulate evolutionary processes such as horizontal gene transfer and gene recombination …
reticulate evolutionary processes such as horizontal gene transfer and gene recombination …
Phylo2Vec: a vector representation for binary trees
Binary phylogenetic trees inferred from biological data are central to understanding the
shared history among evolutionary units. However, inferring the placement of latent nodes in …
shared history among evolutionary units. However, inferring the placement of latent nodes in …
Brauer and partition diagram models for phylogenetic trees and forests
A Francis, PD Jarvis - Proceedings of the Royal Society …, 2022 - royalsocietypublishing.org
We introduce a correspondence between phylogenetic trees and Brauer diagrams, inspired
by links between binary trees and matchings described by Diaconis and Holmes (1998 Proc …
by links between binary trees and matchings described by Diaconis and Holmes (1998 Proc …
Signatures of natural selection in tree topology shape of serially sampled viral phylogenies
LP Barzilai, CG Schrago - Molecular Phylogenetics and Evolution, 2023 - Elsevier
Tree shape metrics can be computed fast for trees of any size, which makes them promising
alternatives to intensive statistical methods and parameter-rich evolutionary models in the …
alternatives to intensive statistical methods and parameter-rich evolutionary models in the …
Quantifying syntax similarity with a polynomial representation of dependency trees
We introduce a graph polynomial that distinguishes tree structures to represent dependency
grammar and a measure based on the polynomial representation to quantify syntax …
grammar and a measure based on the polynomial representation to quantify syntax …
A polynomial invariant for a new class of phylogenetic networks
Invariants for complicated objects such as those arising in phylogenetics, whether they are
invariants as matrices, polynomials, or other mathematical structures, are important tools for …
invariants as matrices, polynomials, or other mathematical structures, are important tools for …
Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding
P Liu, J Lusk, N Jonoska… - PLOS Computational …, 2024 - journals.plos.org
R-loops are a class of non-canonical nucleic acid structures that typically form during
transcription when the nascent RNA hybridizes the DNA template strand, leaving the non …
transcription when the nascent RNA hybridizes the DNA template strand, leaving the non …
Ranking trees based on global centrality measures
Trees, or connected graphs with no cycles, are a commonly studied combinatorial family.
When many natural metrics on networks are applied to the set of all trees of a fixed order, the …
When many natural metrics on networks are applied to the set of all trees of a fixed order, the …
Revisiting Tree Isomorphism: AHU Algorithm with Primes Numbers
F Ingels - arXiv preprint arXiv:2309.14441, 2023 - arxiv.org
The AHU algorithm has been the state of the art since the 1970s for determining in linear
time whether two unordered rooted trees are isomorphic or not. However, it has been …
time whether two unordered rooted trees are isomorphic or not. However, it has been …