TAR DNA-binding protein 43 (TDP-43) is a prion-like RNA-binding protein that plays a key role in amyotrophic lateral sclerosis and frontotemporal dementia. Producing full-length TDP-43 consistently is thus relevant for its in vitro studies and yet it remains challenging, especially with the current requirement to work under biosafety level-2 (BSL-2) containment due to new safety […]
Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma
Burkitt lymphoma (BL) carries multiple oncogenic drivers yet arises predominantly in children, whose normal cells harbour few age-related mutations. To investigate this paradox, we sought to define the sequence and timing of mutational drivers underlying BL development. Here, we analysed single-cell whole-genome sequencing (WGS) data of 250 paired normal and malignant B-cells from BL patients […]
Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma
Burkitt lymphoma (BL) carries multiple oncogenic drivers yet arises predominantly in children, whose normal cells harbour few age-related mutations. To investigate this paradox, we sought to define the sequence and timing of mutational drivers underlying BL development. Here, we analysed single-cell whole-genome sequencing (WGS) data of 250 paired normal and malignant B-cells from BL patients […]
Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells
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 […]
SEEK-VEC: Robust Latent Structure Discovery via Ensemble Topic Modeling
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, […]
Phylogeny, ecology, and allometry: hierarchical controls of insect elemental composition
Elemental composition links organismal physiology to biogeochemical cycles, yet the relative importance of evolutionary and ecological drivers remains unresolved for insects. Integrating a global stoichiometric database with a comprehensive phylogenetic backbone, we demonstrate hierarchical control of insect stoichiometry, with phylogeny accounting for ~50% of variation in C:N:P ratios, followed by temperature, body mass, trophic group […]
Predicting porcini: a decade of sporocarp monitoring reveals the meteorological triggers of Boletus edulis fruiting in central European beech forests
The reproductive biology of ectomycorrhizal fungi (EMF) is difficult to study because sporocarp formation cannot be reliably induced under laboratory conditions. This limitation partly reflects our incomplete understanding of the short-term meteorological conditions that trigger fruiting in most EMF species. To address this knowledge gap, we analyzed a decade-long (2015-2024) dataset of near-exhaustive sporocarp observations […]
Herbivore pressure modulates soil multifunctionality in a Mediterranean landscape
Ongoing global environmental changes demand cost-effective strategies to restore ecosystem functioning. Within this context, the reintroduction of large mammalian herbivores has emerged as a promising approach to recover ecological processes and foster self-sustaining, biodiverse ecosystems. However, the impacts of such initiatives remain poorly understood, particularly regarding their effects on soil functions and ecological processes. We […]
Transcriptional Activation of Estrogen Receptor-alpha and Estrogen Receptor-beta from Elephant Shark (Callorhynchus milii)
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 […]
PhytClust: efficient and optimal node clustering in phylogenetic trees
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 […]