Quantitative Biology
Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential…
Cardiovascular hemodynamic fields provide valuable medical decision markers for coronary artery disease. Computational fluid dynamics (CFD) is the gold standard for accurate, non-invasive evaluation of these quantities in silico. In this…
Parameter inference and uncertainty quantification are important steps when relating mathematical models to real-world observations, and when estimating uncertainty in model predictions. However, methods for doing this can be…
Recent advances in geometric deep learning and generative modeling have enabled the design of novel proteins with a wide range of desired properties. However, current state-of-the-art approaches are typically restricted to generating…
The mesoderm invagination of the Drosophila embryo is known as an archetypal morphogenic process. To explore the roles of the active cellular forces and the regulation of these forces, we developed an integrated vertex model that combines…
Mild cognitive impairment (MCI) is the prodromal stage of Alzheimer's disease (AD) and thus enrolling MCI subjects to undergo clinical trials is worthwhile. However, MCI groups usually show significant diversity and heterogeneity in the…
In structure-based drug discovery, virtual screening using conventional molecular docking methods can be performed rapidly but suffers from limitations in prediction accuracy. Recently, Boltz-2 was proposed, achieving extremely high…
Spatial proteomics maps protein distributions in tissues, providing transformative insights for life sciences. However, current sequencing-based technologies suffer from low spatial resolution, and substantial inter-tissue variability in…
The comparison of protein structures is a fundamental task in computational biology, crucial for understanding protein function, evolution, and for drug design. While analytical methods like the Kabsch algorithm provide an exact,…
Predictive processing and active inference posit that the brain is a system performing Bayesian inference on the environment. By virtue of this, a prominent interpretation of predictive processing states that the generative model (a POMDP)…
To rapidly coordinate collective behaviors in tissues, cells communicate with one another through traveling fronts of signaling activity called trigger waves. The stimulus threshold for wave propagation is a key biological parameter that…
Network science has been applied widely to study brain network organization, especially at the meso-scale, where nodes represent brain areas and edges reflect interareal connectivity inferred from imaging or tract-tracing data. While this…
Background: Accurate survival prediction in breast cancer is essential for patient stratification and personalized therapy. Integrating gene expression data with clinical factors may enhance prognostic performance and support precision…
Visual impairment impacts more than 2.2 billion people worldwide, and it greatly restricts independent mobility and access. Conventional mobility aids - white canes and ultrasound-based intelligent canes - are inherently limited in the…
Functional connectivity (FC) derived from resting-state fMRI plays a critical role in personalized predictions such as age and cognitive performance. However, applying foundation models(FM) to fMRI data remains challenging due to its high…
Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce…
Live cell culture is crucial in biomedical studies for analyzing cell properties and dynamics in vitro. This study focuses on segmenting unstained live cells imaged with bright-field microscopy. While many segmentation approaches exist for…
The TIM-barrel fold is one of the most versatile and ubiquitous protein folds in nature, hosting a wide variety of catalytic activities and functions while serving as a model system in protein biochemistry and engineering. This review…
The villi and crypts of the gastrointestinal tract increase the effective surface area of the intestinal mucosa, potentially enhancing nutrient absorption. It is commonly assumed that this is their primary function, and that a higher villi…
Recent breakthroughs in single-cell technology have ushered in unparalleled opportunities to decode the molecular intricacy of intricate biological systems, especially those linked to diseases unique to humans. However, these progressions…