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Single-Cell Analysis

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Utilizing machine learning to integrate single-cell and bulk RNA sequencing data for constructing and validating a novel cell adhesion molecules related prognostic model in gastric cancer.

Computers in biology and medicine
BACKGROUND: Cell adhesion molecules (CAMs) play a vital role in cell-cell interactions, immune response modulation, and tumor cell migration. However, the unique role of CAMs in gastric cancer (GC) remains largely unexplored.

Quantitative Three-Dimensional Imaging Analysis of HfO Nanoparticles in Single Cells via Deep Learning Aided X-ray Nano-Computed Tomography.

ACS nano
It is crucial for understanding mechanisms of drug action to quantify the three-dimensional (3D) drug distribution within a single cell at nanoscale resolution. Yet it remains a great challenge due to limited lateral resolution, detection sensitiviti...

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data.

BMC bioinformatics
The recent advances in high-throughput single-cell sequencing have created an urgent demand for computational models which can address the high complexity of single-cell multiomics data. Meticulous single-cell multiomics integration models are requir...

scHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information.

Communications biology
The emergence of single-cell Hi-C (scHi-C) technology has provided unprecedented opportunities for investigating the intricate relationship between cell cycle phases and the three-dimensional (3D) structure of chromatin. However, accurately predictin...

Single-cell hdWGCNA reveals metastatic protective macrophages and development of deep learning model in uveal melanoma.

Journal of translational medicine
BACKGROUND: Although there has been some progress in the treatment of primary uveal melanoma (UVM), distant metastasis remains the leading cause of death in patients. Monitoring, staging, and treatment of metastatic disease have not yet reached conse...

Elucidating Microglial Heterogeneity and Functions in Alzheimer's Disease Using Single-cell Analysis and Convolutional Neural Network Disease Model Construction.

Scientific reports
In this study, we conducted an in-depth exploration of Alzheimer's Disease (AD) by integrating state-of-the-art methodologies, including single-cell RNA sequencing (scRNA-seq), weighted gene co-expression network analysis (WGCNA), and a convolutional...

Single-cell RNA sequencing data analysis utilizing multi-type graph neural networks.

Computers in biology and medicine
Single-cell RNA sequencing (scRNA-seq) is the sequencing technology of a single cell whose expression reflects the overall characteristics of the individual cell, facilitating the research of problems at the cellular level. However, the problems of s...

Harnessing Artificial Intelligence in Multimodal Omics Data Integration: Paving the Path for the Next Frontier in Precision Medicine.

Annual review of biomedical data science
The integration of multiomics data with detailed phenotypic insights from electronic health records marks a paradigm shift in biomedical research, offering unparalleled holistic views into health and disease pathways. This review delineates the curre...

Contextual AI models for single-cell protein biology.

Nature methods
Understanding protein function and developing molecular therapies require deciphering the cell types in which proteins act as well as the interactions between proteins. However, modeling protein interactions across biological contexts remains challen...