Related papers: Genomic data analysis in tree spaces
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
As costs of genome sequencing have dropped precipitously, development of efficient bioinformatic methods to analyze genome structure and evolution have become ever more urgent. For example, most published phylogenomic studies involve either…
Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of…
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…
Phylogenetic analyses based on small to moderately sized sets of sequential data lead to overestimating mutation rates in influenza hemagglutinin (HA) by at least an order of magnitude. Two major underlying reasons are: the incomplete…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Viral mutations pose significant threats to public health by increasing infectivity, strengthening vaccine resistance, and altering disease severity. To track these evolving patterns, agencies like the CDC annually evaluate thousands of…
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…
We develop a general statistical framework for the analysis and inference of large tree-structured data, with a focus on developing asymptotic goodness-of-fit tests. We first propose a consistent statistical model for binary trees, from…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
We consider the analysis of high dimensional data given in the form of a matrix with columns consisting of observations and rows consisting of features. Often the data is such that the observations do not reside on a regular grid, and the…
Determining phenotype from genetic data is a fundamental challenge. Influenza A viruses undergo rapid antigenic drift and identification of emerging antigenic variants is critical to the vaccine selection process. Using former seasonal…
Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and re-infect previously infected individuals. Antigenic properties are largely determined by the surface glycoprotein hemagglutinin (HA) and…
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…
The diameter distribution of a given species of deciduous trees in mature, temperate zone forests is well approximated by a Gamma distribution. Here we give new experimental evidence for this conjecture by analyzing deciduous tree size data…
Evolutionary models for populations of constant size are frequently studied using the Moran model, the Wright-Fisher model, or their diffusion limits. When evolution is neutral, a random genealogy given through Kingman's coalescent is used…
Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…