Antimicrobial peptides (AMPs) are key effectors of host defence, however, their functional deployment across renal tissue and urine in pyelonephritis (PN) remains incompletely understood. Here, we integrate kidney and urine proteomics with urinary pe... read more
Mutation-induced drug resistance is a major contributor to the failure of targeted cancer therapies, particularly in tumors driven by mutations in the KRAS oncogene. Although covalent inhibitors effectively target KRAS G12C, secondary mutations such ... read more
Proteins are fundamental macromolecules involved in virtually all biological processes. Their physiological roles are tightly linked to their three-dimensional structure, which can be naturally abstracted as Protein Contact Networks (PCNs), i.e., gra... read more
Despite significant neurobiological and pathological overlaps, Alzheimer's (AD) and Parkinson's (PD)-the primary threats to healthy aging-are still managed as distinct clinical entities. Standard machine learning exacerbates this fragmentation by pri... read more
The classification of pediatric brain tumors is investigated using deep learning on hematoxylin and eosin (H&E) and antigen Ki-67 (Ki-67) whole slide images (WSIs) from the Children's Brain Tumor Network (CBTN) dataset. A total of 1,662 unregistered ... read more
Inferring the selective effects of copy-number alterations (CNAs) from clonal tumor data is essential for understanding tumor evolution. In practice, intra-tumor evolutionary parameters are typically estimated by fitting population genetic models to ... read more
Traditional clonogenic assays remain central to evaluating the self-renewal capacity of tumor cells. However, the assay relies on subjective endpoint measurements, is restricted to two-dimensional monolayer growth, and lacks the single cell resolutio... read more
Characterising equilibrium conformational ensembles with deep generative models requires assessing not only whether a model reproduces the target distribution, but also the mechanism of how it arrives here. Here we examine two distinct routes to gene... read more
A virtual cell is a world model of a cell: a computational system that predicts, simulates and programs cellular processes across modalities and scales. An important path toward this goal is to model how genetic and chemical perturbations give rise t... read more
Current single-cell foundation models rely on language-model architectures that ignore transcriptomic data distributions, often underperforming specialized methods. We introduce xVERSE, a transcriptomics-native foundation model coupling batch-invaria... read more
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