AIMC Topic: Single-Cell Analysis

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scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework.

Cell genomics
Transcriptome-wide association studies (TWASs) help identify disease-causing genes but often fail to pinpoint disease mechanisms at the cellular level because of the limited sample sizes and sparsity of cell-type-specific expression data. Here, we pr...

Single-cell mitochondrial morphomics reveals cellular heterogeneity and predicts complex I, III, and ATP synthase Inhibition responses.

Scientific reports
Mitochondrial heterogeneity drives diverse cellular responses in neurodegenerative diseases, complicating the evaluation of mitochondrial dysfunction. In this study, we describe a high-throughput imaging and analysis approach to investigate cell-to-c...

Single-cell RNA sequencing reveals immunological link between house dust mite allergy and childhood asthma.

Scientific reports
Allergic asthma in children is typically associated with house dust mites (HDM) as the key allergen. Nevertheless, the diagnostic rate remains below 60% due to the absence of specific symptoms and diagnostic markers, which hinders the implementation ...

Single-cell and spatial transcriptomics reveals an anti-tumor neutrophil subgroup in microwave thermochemotherapy-treated lip cancer.

International journal of oral science
Microwave thermochemotherapy (MTC) has been applied to treat lip squamous cell carcinoma (LSCC), but a deeper understanding of its therapeutic mechanisms and molecular biology is needed. To address this, we used single-cell transcriptomics (scRNA-seq...

Effect of Cell-Cell Interaction on Single-Cell Behavior Revealed by a Deep Learning-Aided High-Throughput Addressable Single-Cell Coculture System.

Analytical chemistry
Cell-cell interactions are crucial for understanding various physiological and pathological processes, yet conventional population-level methods fail to disclose the heterogeneity at a single-cell resolution. Single-cell coculture systems that isolat...

scMUSCL: multi-source transfer learning for clustering scRNA-seq data.

Bioinformatics (Oxford, England)
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) analysis relies heavily on effective clustering to facilitate numerous downstream applications. Although several machine learning methods have been developed to enhance single-cell clustering, most a...

scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery.

Briefings in bioinformatics
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) produces vast amounts of individual cell profiling data. Its analysis presents a significant challenge in accurately annotating cell types and their associated biomarkers. Different pipelines ...

Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering.

Briefings in bioinformatics
Clustering is pivotal in deciphering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data. However, it suffers from several challenges in handling the high dimensionality and complexity of scRNA-seq data. Especially when employing gr...

Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data.

Briefings in bioinformatics
Single-cell sequencing has advanced our understanding of cellular heterogeneity and disease pathology, offering insights into cellular behavior and immune mechanisms. However, extracting meaningful phenotype-related features is challenging due to noi...