Quantitative Biology
Fossil DNA preservation varies with depositional environments and diagenesis, producing fragments of heterogeneous origins and degradation states. We use first-principles biomolecular analysis to classify fossil molecular environments into…
The NBSS (normalized biomass size spectrum) is a common, intuitive approach for the study of natural ecosystems. However, very few studies have been dedicated to verifying possible flaws and paradoxes in this widely used method. Evident…
We present FLOWR.root, an SE(3)-equivariant flow-matching model for pocket-aware 3D ligand generation with joint potency and binding affinity prediction and confidence estimation. The model supports de novo generation, interaction- and…
The use of ad-hoc engineered viruses in the fight against tumours is one of the greatest ideas in cancer therapeutics within the last three decades. Together with other strategies such as immunotherapies, nanoparticles and adjunct…
Boolean networks are a widely used modeling framework in systems biology for studying gene regulation, signal transduction, and cellular decision-making. Empirical studies indicate that biological Boolean networks exhibit a high degree of…
People make strategic decisions many times a day - during negotiations, when coordinating actions with others, or when choosing partners for cooperation. The resulting dynamics can be studied with learning theory and evolutionary game…
Species complexes are groups of closely related populations exchanging genes through dispersal. We study the dynamics of the structure of species complexes in a class of metapopulation models where demes can exchange genetic material…
We develop a novel ultrasound nasogastric tube (UNGT) dataset to address the lack of public nasogastric tube datasets. The UNGT dataset includes 493 images gathered from 110 patients with an average image resolution of approximately 879…
The effectiveness of oncolytic virotherapy is significantly affected by several elements of the tumour microenvironment, which reduce the ability of the virus to infect cancer cells. In this work, we focus on the influence of hypoxia on…
This proof-of-concept study introduces a novel multimodal framework combining synchronized EEG-fNIRS modalities with neuronal avalanche analysis to identify early network dysfunction in Alzheimer's disease. The approach leverages…
The disjunction effect in human decision making is often taken to show that the classical law of total probability is violated, motivating quantum-like models. We re-examine this claim for the Prisoner's Dilemma disjunction effect. Under…
Mechanical loading in articular cartilage drives interstitial fluid flow through the porous collagen proteoglycan matrix, generating electrokinetic signals. We investigate whether the structural organization of cartilage histology can be…
Alzheimer's disease (AD) develops over a prolonged preclinical phase, during which neuropathological changes accumulate long before cognitive symptoms appear. Identifying cognitive functions affected at early stages is critical for the…
The incorporation of neuroimaging techniques such as electroenchephalography (EEG) and functional near-infrared spectroscopy (fNIRS) has provided new opportunities for the analysis of dynamic brain processes involved in cognitive and motor…
Musculoskeletal injuries (MSI) in Thoroughbred racehorses are a leading cause of death and premature retirement in racehorses and are heavily influenced by training practices. Greater distances of high-speed galloping accumulated during…
Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent…
Accurate prediction of synthetic lethality (SL) is important for guiding the development of cancer drugs and therapies. SL prediction faces significant challenges in the effective fusion of heterogeneous multi-source data. Existing…
Aphasia, a language impairment primarily resulting from stroke or brain injury, profoundly disrupts communication and everyday functioning. Despite advances in speech therapy, barriers such as limited therapist availability and the scarcity…
Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret…
Fluorescence-based Ca$^{2+}$-imaging is a powerful tool for studying localized neuronal activity, including miniature Synaptic Calcium Transients, providing real-time insights into synaptic activity. These transients induce only subtle…