Quantitative Biology
The collective frequency that emerges from synchronized neuronal populations--the network resonance--shows a systematic relationship with brain size: whole-brain's large networks oscillate slowly, whereas finer parcellations of fixed volume…
Biomolecular interaction modeling has been substantially advanced by foundation models, yet they often produce all-atom structures that violate basic steric feasibility. We address this limitation by enforcing physical validity as a strict…
The automated extraction of chemical structures and their corresponding bioactivity data is essential for accelerating drug discovery and enabling data-driven research. Current optical chemical structure recognition tools lack the…
RNA structure determination is essential for understanding its biological functions. However, the reconstruction process often faces challenges, such as atomic clashes, which can lead to inaccurate models. To address these challenges, we…
Many fundamental parameters of biological systems -- eg. productivity, population sizes and biomass -- are most effectively expressed in absolute terms. In contrast to proportional data (eg. percentages), absolute values provide…
Replicating systems sustained by error-prone enzymatic amplification can undergo critical transitions between persistence and extinction. In RNA viruses, such transitions are classically governed by mutation rates and fitness landscapes,…
Representation learning for protein biochemical space faces a difficult trade-off: protein language models excel at capturing long-range biological semantics but often miss fine-grained chemical details. Conversely, chemical language models…
Background: Klebsiella pneumoniae is a major opportunistic pathogen responsible for various invasive infections. The rise of carbapenem-resistant K. pneumoniae, primarily due to acquisition of bla NDM genes, presents a serious global health…
Ecological interaction networks are rarely homogeneous: species naturally form communities with distinct interaction structures, resulting in block-structured variance and correlation profiles in the interaction matrix. We study the…
One of the main goals of artificial life research is to recreate in artificial systems the trends for ever more complex and novel entities, interactions and processes that we see in Earth's biosphere, that is, to create open-ended systems.…
Bladder function is typically assessed through pressure volume relations, compliance indices and flow measurements, whereas structural evaluation relies largely on qualitative imaging findings. These approaches do not formally quantify how…
Effective wound repair treatments rely on a clear picture of how cell proliferation and migration are coordinated during tissue restoration. Fibroblasts are key contributors to tissue restoration in the dermis, and modern imaging tools…
Understanding the mechanisms that govern species coexistence and biodiversity represents a fundamental challenge in ecology. This study extends the classic rock-paper-scissors model by introducing a context-dependent higher-order…
A colony of the queenless ant species, \emph{Pristomyrmex punctatus}, can broadly be seen as consisting of small-body sized worker ants and relatively larger body-sized cheater ants. Hence, in the presence of inter-colony migration, a set…
Understanding how long-term stimulation reshapes neural circuits requires uncovering the rules of brain plasticity. While short-term synaptic modifications have been extensively characterized, the principles that drive circuit-level…
Background. Breast cancer comprises at least five molecular subtypes with distinct prognoses, yet PAM50 classification relies on transcriptomics alone. Whether integrating DNA methylation and copy number data improves subtype recovery and…
Objective: ML-based clinical risk prediction models are increasingly used to support decision-making in healthcare. While class-imbalance correction techniques are commonly applied to improve model performance in settings with rare…
Computational pathology models that use digitized histopathology whole-slide images have the potential to become a cost-effective and scalable alternative to molecular assays for the prediction of genomic biomarkers, a key task in precision…
Adverse Drug Reactions (ADRs) are a leading cause of morbidity and mortality. Existing prediction methods rely mainly on chemical similarity, machine learning on structured databases, or isolated target profiles, but often fail to integrate…
The ribosome is responsible for protein synthesis in all cells, and is the largest energy consumer in the cell. We propose that the ribosome originated as a mutualistic symbiont of an RNA-dependent RNA polymerase ribozyme, supplying…