Related papers: Quantifying Reticulation in Phylogenetic Complexes…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
Within the context of topological data analysis, the problems of identifying topological significance and matching signals across datasets are important and useful inferential tasks in many applications. The limitation of existing solutions…
In this paper, we consider topological featurizations of data defined over simplicial complexes, like images and labeled graphs, obtained by convolving this data with various filters before computing persistence. Viewing a convolution…
Interacting, self-propelled particles such as epithelial cells can dynamically self-organize into complex multicellular patterns, which are challenging to classify without a priori information. Classically, different phases and phase…
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
We introduce Reeb complexes in order to capture how generators of homology flow along sections of a real valued continuous function. This intuition suggests a close relation of Reeb complexes to established methods in topological data…