Quantitative Biology
Bioinformatics web servers are critical resources in modern biomedical research, facilitating interactive exploration of datasets through custom-built interfaces with rich visualization capabilities. However, this human-centric design…
Fibroblast cells play a key role in maintaining the extracellular matrix. During wound healing, fibroblasts differentiate into highly contractile myofibroblasts, which secrete extracellular matrix proteins like collagen to facilitate tissue…
Across the life sciences, an ongoing effort over the last 50 years has made data and methods more reproducible and transparent. This openness has led to transformative insights and vastly accelerated scientific progress. For example,…
Exact stochastic simulation of continuous-time Markov chains (CTMCs) is essential when discreteness and noise drive system behavior, but the hard categorical event selection in Gillespie-type algorithms blocks gradient-based learning. We…
Atherosclerotic plaques are fatty, cellular lesions that form in artery walls. The early plaque contains monocyte-derived macrophages, which are recruited to consume locally bound lipid deposits. Plaque progression is characterised by an…
Background: KRAS mutations are the largest oncogenic subset in NSCLC. While KRAS G12C is now targetable, no approved therapies exist for G12D. We examined time-to-next-treatment (TTNT) and overall survival (OS) differences between G12C and…
Despite significant analysis of bird flight, generative physics models for flight dynamics do not currently exist. Yet the underlying mechanisms responsible for various flight manoeuvres are important for understanding how agile flight can…
EEG-based neural decoding models often fail to generalize across acquisition sites due to structured, site-dependent biases implicitly exploited during training. We reformulate cross-site clinical EEG learning as a bias-factorized…
Theoretical ecology has traditionally equated persistence with the stability of a fixed equilibrium point. Here we argue that the primary threat to ecosystem persistence need not be the loss of stability, but instead the escape of the…
We obtain bounds on the Kullback--Leibler divergence to equilibrium for mass-action chemical reaction networks (CRNs) with equilibrium. The associated decay rates are characterized in terms of the singular values of the stoichiometric…
Adeno-associated viruses (AAVs) are promising vectors for gene therapy, but their native serotypes face limitations in tissue tropism, immune evasion, and production efficiency. Engineering capsids to overcome these hurdles is challenging…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
Coordinating multi-articulated bodies to generate purposeful movement is a formidable computational challenge. Yet the human motor system performs this task robustly in dynamic, uncertain environments, despite noisy and delayed feedback,…
The white matter of the brain is organised into axonal bundles that support long-range neural communication. Although diffusion MRI (dMRI) enables detailed mapping of these pathways through tractography, how white matter pathways directly…
How does the brain predict physical outcomes while acting in the world? Machine learning world models compress visual input into latent spaces, discarding the spatial structure that characterizes sensory cortex. We propose isomorphic world…
The deployment of wearable-based health prediction systems has accelerated rapidly, yet these systems face a fundamental challenge: they generate alerts under substantial uncertainty without principled mechanisms for user-specific…
Protein-ligand scoring is a central component of structure-based drug design, underpinning molecular docking, virtual screening, and pose optimization. Conventional physics-based energy functions are often computationally expensive,…
The representation of protein backbone geometry through the discrete nonlinear Schr\"odinger equation provides a theoretical connection between biological structure and integrable systems. Although the global application of this framework…
Multiple phenotypic protein expressions arising from one genome represent variations in the protein relative abundance and their stoichiometry. A lack of definite compositional parts challenges the modeling of protein megacomplexes and…
The computational design of antibodies with high specificity and affinity is a cornerstone of modern therapeutic development. While deep generative models have demonstrated potential, they often struggle to balance high-fidelity geometric…