定量方法
Behaviour change lies at the heart of many observable collective phenomena such as the transmission and control of infectious diseases, adoption of public health policies, and migration of animals to new habitats. Representing the process…
Human metapneumovirus (hMPV) poses serious risks to pediatric, elderly, and immunocompromised populations. Traditional antibody discovery pipelines require 10-12 months, limiting their applicability for rapid outbreak response. This project…
While linear registration is a critical step in MRI preprocessing pipelines, its numerical uncertainty is understudied. Using Monte-Carlo Arithmetic (MCA) simulations, we assessed the most commonly used linear registration tools within…
The microtubule cytoskeleton is comprised of dynamic, polarized filaments that facilitate transport within the cell. Polarized microtubule arrays are key to facilitating cargo transport in long cells such as neurons. Microtubules also…
In many species of songbirds, juvenile males learn their songs from adult male tutors. In this paper we formulate a novel Markov model for birdsong transmission developed by analogy with models used in biological sequence analysis. We fit…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
As the global population continues to age, there is an increasing demand for ways to accurately quantify the biological processes underlying aging. Biological age, unlike chronological age, reflects an individual's physiological state,…
CRISPR-based genome editing has revolutionized biotechnology, yet optimizing guide RNA (gRNA) design for efficiency and safety remains a critical challenge. Recent advances (2020--2025, updated to reflect current year if needed) demonstrate…
Tree rings provide long-term records of tree growth and climate changes, which makes them ideal benchmarks for forest modeling. Tree-ring information has greatly improved the reliability of 3-PG, which is one of the most commonly used…
Modeling forest dynamics under novel climatic conditions requires a careful balance between process-based understanding and empirical flexibility. Dynamic Vegetation Models (DVM) represent ecological processes mechanistically, but their…
Foundation models have recently emerged as powerful feature extractors in computational pathology, yet they typically omit mechanisms for leveraging the global spatial structure of tissues and the local contextual relationships among…
This study introduces a novel method for quantifying challenging carotenoids in leaf tissues, which typically produce less stable signals than fruits, grains, and roots, by applying Linear Discriminant Analysis (LDA) modeling to interpret…
One-dimensional (1D) blood flow simulations are extensively used in cardiovascular research due to their computational efficiency and effectiveness in analyzing pulse wave dynamics. Despite their versatility and simplicity, there is a lack…
Genomic language models (gLMs) hold promise for generating novel, functional DNA sequences for synthetic biology. However, realizing this potential requires models to go beyond evolutionary plausibility and understand how DNA sequence…
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…
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…
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,…