Philaenus spumarius (L.), the meadow spittlebug, is the principal European vector of Xylella fastidiosa. This xylem-feeding insect has a broad host range, ecological plasticity, and mobility, making it an efficient vector across diverse landscapes. Yet, major gaps remain in understanding its genetic diversity, migration patterns, and local adaptation, limiting effective control of X. fastidiosa outbreaks. […]

The Bryopsidales, a group of siphonous green algae, are of particular evolutionary interest due to their unusual cellular organization and striking morphological and ecological diversity. There are indications for genome duplication, but low taxon sampling has limited our insights of these processes and how they may contribute to these traits. The relationships among certain bryopsidalean […]

Phylogenetic trees play a fundamental role in elucidating evolutionary relationships among taxa. Clustering taxa remains a major challenge across diverse biological domains such as cancer genomics, microbial systematics, and phylogenomics. Several methods partition taxa in phylogenetic trees into clusters, but these approaches face key limitations. Many rely on arbitrary distance thresholds that are contingent on […]

Molecular clock and preservation of early microfossil assemblages suggest that eukaryotes were present and already diverse more than ~1600 million years ago (Ma). Yet, the earliest identifiable eukaryotic crown group fossil only appeared around 1050 Ma, leaving a ~600 million years gap in the Mesoproterozoic during which the evolution and diversification of early eukaryotes remain […]

Humans and other terrestrial vertebrates contain two estrogen receptors (ERs), ER-alpha and ER-beta. Among cartilaginous fish (sharks, rays, skates), which are jawless vertebrates that evolved about 525 million years ago, only activation by steroids of ER-beta orthologs has been character-ized. To remedy this gap in understanding estrogen signaling in jawless vertebrates, we studied estrogen activation […]

Hosts and viruses are in a constant evolutionary arms race, in which viruses physically interact with many host proteins (immune and non-immune) in order to replicate. Here, we manually classify ~2,500 human virus interacting proteins (VIPs) as a function of their involvement during specific viral replication steps in order to quantify host adaptation across the […]

We investigate a spatially explicit metapopulation model consisting of one predator and two hierarchically competing prey species on a discrete lattice. Each local population follows stochastic rules for extinction, colonisation, competition, and predation. From the master equation of this individual-based model, we rigorously derive the corresponding mean-field equations. The analysis of these first-principles mean-field equations […]

The budding yeast Saccharomyces cerevisiae is a well-established model for studying the genetic basis of complex traits, and it is a powerful system for investigating mechanisms of aging. Here, we examine the genomic and transcriptomic factors contributing to increased replicative age in recombinant yeast populations harboring standing genetic variation. Using Fluorescence-Activated Cell Sorting (FACS), we […]

Count data are ubiquitous across many applications in which understanding hidden patterns, or latent structure, is of interest. Topic modeling is a powerful tool for detecting latent structure in count data. However, standard topic modeling methods are often constrained by their restrictive assumptions, susceptible to noise, and sensitive to misspecification of the number of topics, […]

Primary human myeloid cells are promising candidates for immunotherapy, yet efficient and scalable technologies for genetic engineering and screening in these cells are limited. Here we present a virus-like particle (VLP)-based toolkit that delivers diverse CRISPR genome editing modalities to human monocytes, macrophages, and dendritic cells with high efficiency while preserving viability and innate immune […]