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Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
The evolutionary processes of complex systems contain critical information regarding their functional characteristics. The generation time of edges provides insights into the historical evolution of various networked complex systems, such…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
Large-scale structural patterns commonly occur in network models of complex systems including a skewed node degree distribution and small-world topology. These patterns suggest common organizational constraints and similar functional…
Introgression is an evolutionary process in which genes or other types of genetic material are introduced into a genome. It is an important evolutionary process that can, for example, play a fundamental role in speciation. Recently the…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset. Storing and sharing such large collection of…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Population structure can be modelled by evolutionary graphs, which can have a substantial, but very subtle influence on the fate of the arising mutants. Individuals are located on the nodes of these graphs, competing with each other to…
Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
Recently, as the spread of smart devices increases, the amount of data collected through sensors is increasing. A lifelog is a kind of big data to analyze behavior patterns in the daily life of individuals collected from various smart…
An emerging area of research is the study of macroscale migration patterns as a network of nodes that represent places (e.g., countries, cities, and rural areas) and edges that encode migration ties that connect those places. In this…
This paper describes GeoPl@ntNet, an interactive web application designed to make Essential Biodiversity Variables accessible and understandable to everyone through dynamic maps and fact sheets. Its core purpose is to allow users to explore…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…