Related papers: Reconstructing Biological and Digital Phylogenetic…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Using (a,b)-trees as an example, we show how to perform a parallel split with logarithmic latency and parallel join, bulk updates, intersection, union (or merge), and (symmetric) set difference with logarithmic latency and with information…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
We investigate active learning by pairwise similarity over the leaves of trees originating from hierarchical clustering procedures. In the realizable setting, we provide a full characterization of the number of queries needed to achieve…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Recent work showed that compiling functional programs to use dense, serialized memory representations for recursive algebraic datatypes can yield significant constant-factor speedups for sequential programs. But serializing data in a…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Existing parallel algorithms for wavelet tree construction have a work complexity of $O(n\log\sigma)$. This paper presents parallel algorithms for the problem with improved work complexity. Our first algorithm is based on parallel integer…
Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
Graph reconstruction can efficiently detect the underlying topology of massive networks such as the Internet. Given a query oracle and a set of nodes, the goal is to obtain the edge set by performing as few queries as possible. An algorithm…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
Efficient embedding virtual clusters in physical network is a challenging problem. In this paper we consider a scenario where physical network has a structure of a balanced tree. This assumption is justified by many real- world…
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
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…
We report on the process of taking an early 2000's mathematical library, the Small Phylogenetic Trees, and transforming it into a FAIR, modern, and sustainable repository for data from algebraic phylogenetics. This process is based on a…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…