Related papers: A Guide to Tracking Phylogenies in Parallel and Di…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
Understanding mobility, movement, and interaction in archaeological landscapes is essential for interpreting past human behavior, transport strategies, and spatial organization, yet such processes are difficult to reconstruct from static…
Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low…
Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Computational models are invaluable in capturing the complexities of real-world biological processes. Yet, the selection of appropriate algorithms for inference tasks, especially when dealing with real-world observational data, remains a…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
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…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…