定量生物学
Protein--ligand docking is widely used in structure-based discovery, but routine studies often fail at the workflow level rather than at the scoring level. Receptor cleaning, ligand preparation, file conversion, box definition, run…
Neuroscientists and computer vision researchers use model-brain alignment benchmarks to compare artificial and biological vision systems. These benchmarks rank models according to alignment measures such as the similarity of…
Mutational signatures describe the pattern of mutations over the different mutation types. Each mutation type is determined by a base substitution and the flanking nucleotides to the left and right of that base substitution. Due to the…
Pancreatic tumor segmentation in contrast-enhanced computed tomography (CT) is clinically important yet technically challenging: lesions are often small, heterogeneous, and easily confused with surrounding soft tissue, and models that…
A comprehensive analysis of viral mutations is essential for understanding viral evolution, disease epidemiology, diagnosis, drug resistance, etc. However, challenges remain in capturing complex mutation patterns and supporting diverse…
Objective: This study aimed to assess how wearable physiological signals, alone and combined with salivary cortisol, distinguish physical and psychological stress and their recovery states. Methods: Six healthy adults completed three…
This paper introduces Resonance Complexity Theory (RCT), which proposes that consciousness emerges from stable interference patterns of oscillatory neural activity. These patterns, shaped by recursive feedback and constructive interference,…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
We present the unified computational framework for modeling the sulcal patterns of human brain obtained from the magnetic resonance images. The Wasserstein distance is used to align the sulcal patterns nonlinearly. These patterns are…
Motivation: Protein function prediction is a challenging task and an open problem in computational biology. The Critical Assessment of protein Function Annotation (CAFA) is a triennial, community-driven initiative that provides an…
Recognizing individual animals over time is central to many ecological and conservation questions, including estimating abundance, survival, movement, and social structure. Recent advances in automated identification from images and even…
Lateral predictive coding (LPC) is a simple theoretical framework to appreciate feature detection in biological neural circuits. Recent theoretical work [Huang et al., Phys.Rev.E 112, 034304 (2025)] has successfully constructed optimal LPC…
Designing regulatory DNA elements with precise cell-type-specific activity is broadly relevant for cell engineering and gene therapy. Deep generative models can generate functional gene-regulatory elements, but existing methods struggle to…
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new functions (i.e. emergence). Here, we…
Virtual cell modeling predicts molecular state changes under genetic perturbations in silico, which is essential for biological mechanism studies. However, existing approaches suffer from unconstrained reasoning, uninterpretable…
The integration of single-cell proteomic data is often hindered by the fragmented nature of targeted antibody panels. To address this limitation, we introduce scpFormer, a transformer-based foundation model designed for single-cell…
Cell proliferation and cell movement are fundamentally stochastic processes which lead to variability in the growth and spatial structure of cell populations in many biological settings, such as cell invasion, wound healing, and tumour…
The onset of life is often framed around membrane bound compartments and encoded metabolism, leaving unresolved how spatial organization arose before stable boundaries. In this context, environmental gradients are usually treated as…
Infectious diseases continue to pose significant public health challenges worldwide, requiring effective prevention and control strategies to mitigate their negative impact. Infectious diseases can be broadly classified into two groups:…
Absolute concentration robustness (ACR) means the concentration of certain species stays the same in all the steady states. In this work, we study how conservation laws might effect non-vacuous ACR in reaction networks. The goal is to show…