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In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…
The decline in ecological connections signifies the potential extinction of species, which can be attributed to disruptions and alterations. The decrease in interconnections among species reflects their susceptibility to changes. For…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
The explosion of data throughout the biomedical sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression, but harnessing these large and diverse datasets remains challenging. Here, we…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution, and have been hypothesized to influence…
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…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
The intrinsic complexity of human biology presents ongoing challenges to scientific understanding. Researchers collaborate across disciplines to expand our knowledge of the biological interactions that define human life. AI methodologies…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…
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…
Dispersal is a well recognized driver of ecological and evolutionary dynamics, and simultaneously an evolving trait. Dispersal evolution has traditionally been studied in single-species metapopulations so that it remains unclear how…
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…
Measuring gene expression simultaneously in both hosts and symbionts offers a powerful approach to explore the biology underlying species interactions. Such dual or simultaneous RNAseq approaches have primarily been used to gain insight…
We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In…