定量方法
Mammalian sleep is characterized by multiple alternations between episodes of rapid-eye-movement sleep (REMS) and non-REM sleep (NREMS). While the mechanisms governing the timing of these ultradian NREMS-REMS cycles remain poorly…
Interpreting gene clusters from RNA sequencing (RNA-seq) remains challenging, especially in antimicrobial resistance studies where mechanistic insight is important for hypothesis generation. Existing pathway enrichment methods can summarize…
Postprandial glucose collected through continuous glucose monitoring (CGM) provides critical information for assessing metabolic capacity and guiding dietary recommendations. Traditional approaches summarize these data into scalar measures,…
Prion-like propagation of misfolded proteins is a key mechanism underlying the progression of neurodegenerative diseases such as Alzheimer's disease. In previous work, we introduced the HeMiTo framework, describing these prion-like dynamics…
The mycelium of a filamentous fungus is a growing, branching network of numerous entangled hyphae exhibiting polarised apical growth. Expansion occurs during the vegetative phase from a single ascospore, driven by the need to explore and…
Mathematical models of natural and man-made systems often have many adjustable parameters that must be estimated from multiple, potentially conflicting datasets. Rather than reporting a single best-fit parameter vector, it is often more…
FcsIT is a platform-independent, open-source tool for calculating the correlation and fitting fluorescence correlation spectroscopy data. The software is written in Python and uses a powerful Dear PyGUI engine for its interface. It provides…
1. Climate change is altering plant phenology globally with potential deleterious impacts on animal species and entire ecosystems, yet the long-term effects of climate change on tropical leaf production remain poorly understood. 2. We…
Cardiovascular-Kidney-Metabolic (CKM) syndrome represents a growing public health crisis, yet the subclinical heterogeneity of its component systems remains underexplored. Early detection of physiological deviation is critical for…
Quantitatively mapping three-dimensional (3D) flow, diffusion, and particle density in crowded living cells remains challenging because most dynamic optical microscopy measurements are effectively planar and existing analysis methods…
Background: Medical Digital Twins (MDTs) are computational representations of individual patients that integrate clinical, genomic, and physiological data to support diagnosis, treatment planning, and outcome prediction. However, most MDTs…
Prediction of genetic biomarkers, e.g., microsatellite instability in colorectal cancer is crucial for clinical decision making. But, two primary challenges hamper accurate prediction: (1) It is difficult to construct a pathology-aware…
Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful…
Mathematical models support inference and forecasting in ecology and epidemiology, but results depend on the estimation framework. We compare Bayesian and Frequentist approaches across three biological models using four datasets:…
For more than two decades, advances in personalised medicine and precision healthcare have largely been based on genomics and other omics data. These strategies aim to tailor interventions to individual patient profiles, promising greater…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
The rapid scaling of Protein Language Models (PLMs) has unlocked unprecedented accuracy in protein structure prediction and design, but the quadratic memory growth of the Key-Value (KV) cache during inference remains a prohibitive barrier…
Protein structural ensembles from NMR spectroscopy capture biologically important conformational heterogeneity, but it remains difficult to determine whether observed variation reflects coordinated motion or noise-like artifacts. We…
When designing control strategies for an infectious disease it is critical to identify the key pathways of transmission. Data on infected hosts - when they were born, where they lived and with whom they interacted - can help infer sources…
Patients with rare types of melanoma such as acral, mucosal, or uveal melanoma, have lower survival rates than patients with cutaneous melanoma; these lower survival rates reflect the lower objective response rates to immunotherapy compared…