Quantitative Biology

Technological advances in the past decades have begun to enable neuroscientists to address fundamental questions about consciousness in an unprecedented way. Here we review remarkable recent progress in our understanding of cellular-level…

Herbal compounds present complex toxicity profiles that are often influenced by both intrinsic chemical properties and pharmacokinetics (PK) governing absorption and clearance. In this study, we develop a quantum regression model to predict…

We have previously shown in model studies that rapid quenches of systems of monomers interacting to form polymer chains can fix nonequilibrium chemistries which could lead to the origin of life. We suggested that such quenching processes…

Sampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets. We introduce PocketVina, a fast and memory-efficient, search-based docking framework…

At the end of the 19th century, Rayleigh and Plateau explained the physical principle behind the fragmentation of a liquid jet into regular droplets commonly observed in everyday life from a faucet. The classical Rayleigh-Plateau…

Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, computation of physico-chemical…

Tuberculosis (TB) continues to pose a major public health challenge, particularly in high-burden regions such as Ethiopia, necessitating a more profound understanding of its transmission dynamics. In this study, we developed an SVEITRS…

Geometric graph neural networks (GNNs) that respect E(3) symmetries have achieved strong performance on small molecule modeling, but they face scalability and expressiveness challenges when applied to large biomolecules such as RNA and…

In this paper, a neural mass perceptual decision making model introduced by Piska{\l}a et al. is analyzed. The model describes activity of two neuron populations influenced by each other and external inputs. The groups' activities…

We develop a minimal whole-heart model that describes cardiac electrical conduction and simulate a basic three-lead electrocardiogram (ECG). We compare our 3-lead ECG model with clinical data from a Norwegian athlete database. The results…

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of…

Quasispecies theory provides the conceptual and theoretical bases for describing the dynamics of biological information of replicators subject to large mutation rates. This theory, initially conceived within the framework of prebiotic…

Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can give rise to very different data…

Now published in Nature Human Behavior doi: https://doi.org/10.1038/s41562-025-02252-z Human vision is mediated by a complex interconnected network of cortical brain areas that jointly represent visual information. While these areas are…

INTRODUCTION: The pharmacological treatment of Major Depressive Disorder (MDD) relies on a trial-and-error approach. We introduce an artificial intelligence (AI) model aiming to personalize treatment and improve outcomes, which was deployed…

In natural ecosystems, species can be characterized by the nonlinear density-dependent self-regulation of their growth profile. Species of many taxa show a substantial density-dependent reduction for low population size. Nevertheless, many…

Designing reaction pathways that maximize the production of a target compound in a given metabolic network is a fundamental problem in systems biology. In this study, we systematically explore the non-oxidative glycolysis metabolic network,…

Sampling low-energy molecular conformations, spatial arrangements of atoms in a molecule, is a critical task for many different calculations performed in the drug discovery and optimization process. Numerous specialized equivariant networks…

We develop ProxelGen, a protein structure generative model that operates on 3D densities as opposed to the prevailing 3D point cloud representations. Representing proteins as voxelized densities, or proxels, enables new tasks and…

The function and dynamics of the cortex are fundamentally shaped by the specific wiring configurations of its constituent axonal fibers, also known as the connectome. However, many dynamical properties of macroscale cortical activity are…