Quantitative Biology
Conflicting clinical trial results on omega-3 highly unsaturated fatty acids (n-3 HUFA) have prompted uncertainty about their cardioprotective effects. While the VITAL trial found no overall cardiovascular benefit from n-3 HUFA…
This paper details an observation that for more primitive organisms, such as some yeasts, the statistical distribution of the origins of replication sometimes looks remarkably like the distribution of eigenvalues from the Circular…
This paper introduces the Single-Cell Perturbation Prediction Diffusion Model (scPPDM), the first diffusion-based framework for single-cell drug-response prediction from scRNA-seq data. scPPDM couples two condition channels,…
The COVID-19 pandemic forced the rapid development of vaccines and the implementation of mass vaccination programs around the world. However, many hesitated to take the vaccine due to concerns about its effectiveness. By looking at an…
Drug discovery through virtual screening (VS) has become a popular strategy for identifying hits against protein targets. Alongside VS, molecular design further expands accessible chemical space. Together, these approaches have the…
Mangroves modify storm surges with impacts on property damages, but these effects vary spatially and by storm intensity. We use high-resolution, kilometer-scale flood and loss models to examine variability in mangrove effects on surge…
Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers…
Classical models of aphid population dynamics are unable to explain multi-peak patterns in field populations. We consider the variable carrying capacity model (VCM), which can generate such complex multi-peak dynamics, but is also…
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
The accuracy with which the human proprioceptive system estimates hand speed is not well understood. To investigate this, we designed an experiment using hobby-grade mechatronics parts and integrated it as a laboratory exercise in a large…
Games have long been a microcosm for studying planning and reasoning in both natural and artificial intelligence, especially with a focus on expert-level or even super-human play. But real life also pushes human intelligence along a…
The lack of standardization in seizure forecasting slows progress in the field and limits the clinical translation of forecasting models. In this work, we introduce a Python-based framework aimed at streamlining the development, assessment,…
Genome-resolved metagenomics has contributed largely to discovering prokaryotic genomes. When applied to microscopic eukaryotes, challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
The ability to discriminate similar visual stimuli is an important index of memory function. This ability is widely thought to be supported by expanding the dimensionality of relevant neural codes, such that neural representations for…
Electrode density optimization in electroencephalography (EEG)-based Brain-Computer Interfaces (BCIs) requires balancing practical usability against signal fidelity, particularly for source localization. Reducing electrodes enhances…
Electroencephalography (EEG) provides a non-invasive window into brain activity, enabling Brain-Computer Interfaces (BCIs) for communication and control. However, their performance is limited by signal fidelity issues, among which the…
Large pretrained language models have transformed natural language processing, and their adaptation to protein sequences -- viewed as strings of amino acid characters -- has advanced protein analysis. However, the distinct properties of…
This review examines the evidence in the literature for physiological co-modulation during human-animal interaction. The aim of this work is to identify studies that assessed co-modulation via simultaneous measurement of physiological…
Recent breakthroughs in artificial intelligence (AI) are reshaping the way we construct computational counterparts of the brain, giving rise to a new class of ``surrogate brains''. In contrast to conventional hypothesis-driven biophysical…