Quantitative Biology
Sudden changes in environmental conditions can lead to evolutionary shifts not only in the optimal trait value, but also in the diffusion variance under the Ornstein-Uhlenbeck (OU) model. While several methods have been developed to detect…
The grand challenge of protein engineering is the development of computational models that can characterize and generate protein sequences for any arbitrary function. However, progress today is limited by lack of 1) benchmarks with which to…
Neurons process sensory stimuli efficiently, showing sparse yet highly variable ensemble spiking activity involving structured higher-order interactions. Notably, while neural populations are mostly silent, they occasionally exhibit highly…
Ordered leaf attachment, Phylo2Vec, and HOP are three recently introduced vector representations for rooted phylogenetic trees where the representation is determined by an ordering of the underlying leaf set X. Comparing the vectors of two…
Traditional Chinese Medicine diagnosis and treatment principles, established through centuries of trial-and-error clinical practice, directly maps patient-specific symptom patterns to personalised herbal therapies. These empirical holistic…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
A central challenge in Human Immunodeficiency Virus (HIV) public health policy lies in determining whether to universally expand treatment access, despite the risk of sub-optimal adherence and consequent drug resistance, or to adopt a more…
Amateur marathon runners who exercise excessively over time have pathological structural changes in their hearts and aortas. Amateur marathon runners' cardiovascular system adaptations and dangers are discussed in this article. After…
The proton motive force (PMF) across the inner mitochondrial membrane delivers approximately 0.2 eV of energy per proton, powering the FoF1-ATP synthase molecular motor. Here, we provide a detailed accounting of how this energy is utilized:…
Understanding functional diversity, the range and variability of species' roles and actions within their communities, is key to predicting and preserving the functions that sustain both nature and human well-being. In this paper, we provide…
Foundation medical segmentation models, with MedSAM being the most popular, have achieved promising performance across organs and lesions. However, MedSAM still suffers from compromised performance on specific lesions with intricate…
Slow-paced breathing is a promising intervention for reducing anxiety and enhancing emotional regulation through its effects on autonomic and central nervous system function. This study examined the neurophysiological and subjective effects…
Identifying neural markers of stress and cognitive load is key to developing scalable tools for mental state assessment. This study evaluated whether a single-channel high-density EEG (hdrEEG) system could dissociate cognitive and…
SimOmics is an R package designed to generate realistic, multivariate, and multi-omics synthetic datasets. It is intended for use in benchmarking, method development, and reproducibility in bioinformatics, particularly in the context of…
This study presents a seasonally forced cholera model that incorporates imperfect vaccination as a control strategy. The model captures the temporal dynamics of susceptible, vaccinated, infected, and recovered individuals, as well as the…
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
In many neural networks, patterns controlling rhythmic behaviors are maintained across a wide range of periods. In the crustacean pyloric central pattern generator (CPG), a constant bursting pattern is preserved over a three-to-fivefold…
We study how environmental stochasticity influences the long-term population size in certain one- and two-species models. The difficulty is that even when one can prove that there is persistence, it is usually impossible to say anything…
We introduce Ibex, a pan-immunoglobulin structure prediction model that achieves state-of-the-art accuracy in modeling the variable domains of antibodies, nanobodies, and T-cell receptors. Unlike previous approaches, Ibex explicitly…
Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…