Classes of explicit phylogenetic networks and their biological and mathematical significance

S Kong, JC Pons, L Kubatko, K Wicke - Journal of Mathematical Biology, 2022 - Springer
The evolutionary relationships among organisms have traditionally been represented using
rooted phylogenetic trees. However, due to reticulate processes such as hybridization or …

Tree balance indices: a comprehensive survey

M Fischer, L Herbst, S Kersting, L Kühn… - arxiv preprint arxiv …, 2021 - arxiv.org
Tree balance plays an important role in phylogenetics and other research areas, which is
why several indices to measure tree balance have been introduced over the years …

Archaeology and the origins of human cumulative culture: A case study from the earliest Oldowan at Gona, Ethiopia

D Stout, MJ Rogers, AV Jaeggi… - Current …, 2019 - journals.uchicago.edu
The capacity of Homo sapiens for the intergenerational accumulation of complex
technologies, practices, and beliefs is central to contemporary accounts of human …

Advances in computational methods for phylogenetic networks in the presence of hybridization

RAL Elworth, HA Ogilvie, J Zhu, L Nakhleh - … and phylogenetics: seminal …, 2019 - Springer
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate
evolutionary processes such as hybridization. They take the shape of a rooted, directed …

NANUQ: a method for inferring species networks from gene trees under the coalescent model

ES Allman, H Baños, JA Rhodes - Algorithms for Molecular Biology, 2019 - Springer
Species networks generalize the notion of species trees to allow for hybridization or other
lateral gene transfer. Under the network multispecies coalescent model, individual gene …

Total positivity in multivariate extremes

F Röttger, S Engelke, P Zwiernik - The Annals of Statistics, 2023 - projecteuclid.org
Total positivity in multivariate extremes Page 1 The Annals of Statistics 2023, Vol. 51, No. 3,
962–1004 https://doi.org/10.1214/23-AOS2272 © Institute of Mathematical Statistics, 2023 …

Learning and Testing Latent-Tree Ising Models Efficiently

V Kandiros, C Daskalakis, Y Dagan… - The Thirty Sixth …, 2023 - proceedings.mlr.press
We provide time-and sample-efficient algorithms for learning and testing latent-tree Ising
models, ie Ising models that may only be observed at their leaf nodes. On the learning side …

A zero-agnostic model for copy number evolution in cancer

H Schmidt, P Sashittal, BJ Raphael - PLoS computational biology, 2023 - journals.plos.org
Motivation New low-coverage single-cell DNA sequencing technologies enable the
measurement of copy number profiles from thousands of individual cells within tumors. From …

[HTML][HTML] Counting and enumerating tree-child networks and their subclasses

G Cardona, L Zhang - Journal of Computer and System Sciences, 2020 - Elsevier
Galled trees are studied as a recombination model in population genetics. This class of
phylogenetic networks is generalized into tree-child and galled network classes by relaxing …

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

E Gross, L van Iersel, R Janssen, M Jones… - Journal of Mathematical …, 2021 - Springer
Phylogenetic networks can represent evolutionary events that cannot be described by
phylogenetic trees. These networks are able to incorporate reticulate evolutionary events …