Related papers: Visualizing Co-Phylogenetic Reconciliations
Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network…
The visualization of an image collection is the process of displaying a collection of images on a screen under some specific layout requirements. This paper focuses on an important problem that is not well addressed by the previous methods:…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
This paper proposes an embedding method for co-occurrence data aimed at visual information exploration. We consider cases where co-occurrence probabilities are measured between pairs of elements from heterogeneous domains. The proposed…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree…
Extensions of earlier algorithms and enhanced visualization techniques for approximating a correlation matrix are presented. The visualization problems that result from using column or colum--and--row adjusted correlation matrices, which…
Hypergraphs provide a natural way to represent polyadic relationships in network data. For large hypergraphs, it is often difficult to visually detect structures within the data. Recently, a scalable polygon-based visualization approach was…
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…
We study hypergraph visualization via its topological simplification. We explore both vertex simplification and hyperedge simplification of hypergraphs using tools from topological data analysis. In particular, we transform a hypergraph to…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
Network visualization allows a quick glance at how nodes (or actors) are connected by edges (or ties). A conventional network diagram of "contact tree" maps out a root and branches that represent the structure of nodes and edges, often…
Phylogenetic tree reconciliation is employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation.…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
Linear subspace representations of appearance variation are pervasive in computer vision. This paper addresses the problem of robustly matching such subspaces (computing the similarity between them) when they are used to describe the scope…
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…
We study the crossing-minimization problem in a layered graph drawing of planar-embedded rooted trees whose leaves have a given total order on the first layer, which adheres to the embedding of each individual tree. The task is then to…
A witness drawing of a graph is a visualization that clearly shows a given property of a graph. We study and implement various drawing paradigms for witness drawings to clearly show that graphs have bounded pathwidth or treewidth. Our…