Related papers: Popping Bubbles in Pangenome Graphs
Snarls and superbubbles are fundamental pangenome decompositions capturing variant sites. These bubble-like structures underpin key tasks in computational pangenomics, including structural-variant genotyping, distance indexing, haplotype…
Pangenomics uses graph-based models to represent and study the genetic variation between individuals of the same species or between different species. In such variation graphs, a path through the graph represents one individual genome.…
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Superbubbles are acyclic induced subgraphs of a digraph with single entrance and exit that naturally arise in the context of genome assembly and the analysis of genome alignments in computational biology. These structures can be computed in…
We propose a transition-based bubble parser to perform coordination structure identification and dependency-based syntactic analysis simultaneously. Bubble representations were proposed in the formal linguistics literature decades ago; they…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Graph pebbling is a game played on graphs with pebbles on their vertices. A pebbling move removes two pebbles from one vertex and places one pebble on an adjacent vertex. A configuration $C$ is a supply of pebbles at various vertices of a…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
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 distinguishing and working with such objects. In this…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
Probabilistic dependency graphs (PDGs) are a flexible class of probabilistic graphical models, subsuming Bayesian Networks and Factor Graphs. They can also capture inconsistent beliefs, and provide a way of measuring the degree of this…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
A graph puzzle ${\rm Puz}(G)$ of a graph $G$ is defined as follows. A configuration of ${\rm Puz}(G)$ is a bijection from the set of vertices of a board graph to the set of vertices of a pebble graph, both graphs being isomorphic to some…
We propose a clustering-based approach for identifying coherent flow structures in continuous dynamical systems. We first treat a particle trajectory over a finite time interval as a high-dimensional data point and then cluster these data…