定量方法
High-dimensional tissue imaging generates highly complex 3D data containing multiple biomarkers, making it challenging to identify biologically relevant regions without an expert user specifying manual labels for regions of interest. We…
Understanding the intertwined contributions of amino acid sequence and spatial structure is essential to explain protein behaviour. Here, we introduce INFUSSE (Integrated Network Framework Unifying Structure and Sequence Embeddings), a deep…
Fingerprint analysis and fingerprint identification have been the most widely used tools for human identification. To this day, various models have been proposed to explain how fingerprints are formed, ranging from the fibroblast model,…
Background and objective: Prior probability shift between training and deployment datasets challenges deep learning-based medical image classification. Standard correction methods reweight posterior probabilities to adjust prior bias, yet…
EEG-based Brain-Computer Interfaces (BCIs) frequently face spatial specificity limitations in detecting single-trial P300 potentials, a neurophysiological hallmark leveraged for both BCI control and neurodegenerative disease diagnostics. We…
Mathematical oncology is a rapidly evolving interdisciplinary field that uses mathematical models to enhance our understanding of cancer dynamics, including tumor growth, metastasis, and treatment response. Tumor-immune interactions play a…
Identifying evolutionary correspondences between cell types across species is a fundamental challenge in comparative genomics and evolutionary biology. Existing approaches often rely on either reference-based matching, which imposes…
In this methods article, we provide a flexible but easy-to-use implementation of Direct Coupling Analysis (DCA) based on Boltzmann machine learning, together with a tutorial on how to use it. The package \texttt{adabmDCA 2.0} is available…
The key to successful drug design lies in the correct comprehension of protein-ligand interactions. Within the current knowledge paragm, these interactions can be described from both thermodynamic and kinetic perspectives. In recent years,…
Spatial transcriptomics (ST) technologies can be used to align transcriptomes with histopathological morphology, presenting exciting new opportunities for biomolecular discovery. Using ST data, we construct a novel framework, GeneFlow, to…
Geographic atrophy (GA) is a key biomarker of dry age-related macular degeneration (AMD) traditionally identified through color fundus photography. Hyper-transmission defects (hyperTDs), a feature highly correlated with GA, have recently…
Deep generative models provide a promising approach to de novo 3D peptide design. Most of them jointly model the distributions of peptide's position, orientation, and conformation, attempting to simultaneously converge to the target pocket.…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
Single-cell sequencing technology maps cells to a high-dimensional space encoding their internal activity. Recently-proposed virtual cell models extend this concept, enriching cells' representations based on patterns learned from…
Comorbid anxiety disorders are common among patients with major depressive disorder (MDD), but their impact on outcomes of digital and smartphone-delivered interventions is not well understood. This study is a secondary analysis of a…
Collective behaviors in cellular systems are regulated not only by biochemical signalling pathways but also by intercellular mechanical forces, whose quantification in contractile monolayers remains poorly understood. Here, by integrating…
Accurate quantification in positron emission tomography (PET) is essential for accurate diagnostic results and effective treatment tracking. A major issue encountered in PET imaging is attenuation. Attenuation refers to the diminution of…
The identification of bitter peptides is crucial in various domains, including food science, drug discovery, and biochemical research. These peptides not only contribute to the undesirable taste of hydrolyzed proteins but also play key…
Understanding the relationship between antibody sequence, structure and function is essential for the design of antibody-based therapeutics and research tools. Recently, machine learning (ML) models mostly based on the application of large…
Non-invasive colorectal cancer (CRC) screening represents a key opportunity to improve colonoscopy participation rates and reduce CRC mortality. This study explores the potential of the gut-liver axis for predicting colorectal neoplasia…