AIMC Topic: Single-Cell Gene Expression Analysis

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Identification of mitophagy-related biomarkers in severe acute pancreatitis: integration of WGCNA, machine learning algorithms and scRNA-seq.

Frontiers in immunology May 28, 2025
BACKGROUND: Mitophagy is a highly conserved cellular process in eukaryotic cells that selectively clears dysfunctional or damaged mitochondria through autophagy mechanisms to maintain mitochondrial homeostasis. However, the role of mitophagy in the p...
Humans Machine Learning Single-Cell Analysis RNA-Seq Gene Regulatory Networks Single-Cell Gene Expression Analysis Algorithms Biomarkers Animals Gene Expression Profiling Mitophagy Mice Computational Biology Disease Models, Animal Pancreatitis
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scE2EGAE: enhancing single-cell RNA-Seq data analysis through an end-to-end cell-graph-learnable graph autoencoder with differentiable edge sampling.

Biology direct May 27, 2025
BACKGROUND: Single-cell RNA sequencing (scRNA-Seq) technology reveals biological processes and molecular-level genomic information among individual cells. Numerous computational methods, including methods based on graph neural networks (GNNs), have b...
Sequence Analysis, RNA Autoencoder Algorithms Single-Cell Analysis RNA-Seq Single-Cell Gene Expression Analysis Humans Neural Networks, Computer Software
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Integrative Analysis of Lactylation-Associated Features in Abdominal Aortic Aneurysm and Its Immune Microenvironment Utilizing scRNA-seq and Bulk RNA Sequencing.

Circulation journal : official journal of the Japanese Circulation Society Apr 29, 2025
BACKGROUND: Abdominal aortic aneurysm (AAA) is a vascular disease strongly associated with immune dysregulation and metabolic disturbances. Although lactate metabolism and its associated process, lactylation, have been implicated in various diseases,...
Humans Female RNA-Seq Single-Cell Gene Expression Analysis Mice Aged Sequence Analysis, RNA Animals Aortic Aneurysm, Abdominal Male Single-Cell Analysis
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ScAGCN: Graph Convolutional Network with Adaptive Aggregation Mechanism for scRNA-seq Data Dimensionality Reduction.

Interdisciplinary sciences, computational life sciences Apr 25, 2025
With the development of single-cell RNA-sequencing (scRNA-seq) technology, scRNA-seq data analysis suffers huge challenges due to large scale, high dimensionality, high noise, and high sparsity. To achieve accurately embedded representation in the la...
Sequence Analysis, RNA Dimensionality Reduction Single-Cell Analysis RNA-Seq Single-Cell Gene Expression Analysis Computational Biology Humans Neural Networks, Computer Algorithms
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GRLGRN: graph representation-based learning to infer gene regulatory networks from single-cell RNA-seq data.

BMC bioinformatics Apr 18, 2025
BACKGROUND: A gene regulatory network (GRN) is a graph-level representation that describes the regulatory relationships between transcription factors and target genes in cells. The reconstruction of GRNs can help investigate cellular dynamics, drug d...
Single-Cell Gene Expression Analysis Humans Deep Learning Computational Biology Machine Learning Single-Cell Analysis Algorithms Sequence Analysis, RNA RNA-Seq Gene Regulatory Networks
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Molecular features and diagnostic modeling of synovium- and IPFP-derived OA macrophages in the inflammatory microenvironment via scRNA-seq and machine learning.

Journal of orthopaedic surgery and research Apr 17, 2025
BACKGROUND: Osteoarthritis (OA) is the leading cause of degenerative joint disease, with total joint replacement as the only definitive cure. However, no disease-modifying therapy is currently available. Inflammation and fibrosis in the infrapatellar...
Single-Cell Gene Expression Analysis Rats Inflammation Synovial Membrane Rats, Sprague-Dawley Adipose Tissue Osteoarthritis Cellular Microenvironment Male Middle Aged Single-Cell Analysis RNA-Seq Machine Learning Macrophages Female Animals Humans
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Comprehensive analysis of scRNA-seq and bulk RNA-seq data via machine learning and bioinformatics reveals the role of lysine metabolism-related genes in gastric carcinogenesis.

BMC cancer Apr 9, 2025
BACKGROUND: Gastric cancer (GC) is a highly aggressive and heterogeneous cancer with extremely complex biological characteristics. Lysine and its metabolism are closely related to human cancer, but little is known about how lysine metabolism-related ...
Vimentin Gene Regulatory Networks Lysine Single-Cell Gene Expression Analysis Biomarkers, Tumor Computational Biology Humans Gene Expression Regulation, Neoplastic Cell Line, Tumor Machine Learning Sequence Analysis, RNA Nomograms Single-Cell Analysis Prognosis Cell Proliferation RNA-Seq Stomach Neoplasms Carcinogenesis
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scAMZI: attention-based deep autoencoder with zero-inflated layer for clustering scRNA-seq data.

BMC genomics Apr 7, 2025
BACKGROUND: Clustering scRNA-seq data plays a vital role in scRNA-seq data analysis and downstream analyses. Many computational methods have been proposed and achieved remarkable results. However, there are several limitations of these methods. First...
Single-Cell Gene Expression Analysis Computational Biology Sequence Analysis, RNA Cluster Analysis Autoencoder Humans Algorithms Software Deep Learning Single-Cell Analysis RNA-Seq
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scCorrect: Cross-modality label transfer from scRNA-seq to scATAC-seq using domain adaptation.

Analytical biochemistry Mar 27, 2025
Cell type annotation in single-cell chromatin accessibility sequencing (scATAC-seq) is crucial for enabling researchers to identify subpopulations of cells associated with specific diseases, elucidate gene regulatory networks, and discover markers in...
Single-Cell Analysis RNA-Seq Chromatin Humans Single-Cell Gene Expression Analysis Neural Networks, Computer Sequence Analysis, RNA Algorithms
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Development of a MVI associated HCC prognostic model through single cell transcriptomic analysis and 101 machine learning algorithms.

Scientific reports Mar 7, 2025
Hepatocellular carcinoma (HCC) is an exceedingly aggressive form of cancer that often carries a poor prognosis, especially when it is complicated by the presence of microvascular invasion (MVI). Identifying patients at high risk of MVI is crucial for...
Immune Checkpoint Proteins Mutation Carcinoma, Hepatocellular Datasets as Topic Clinical Decision-Making Kaplan-Meier Estimate Treatment Outcome Single-Cell Gene Expression Analysis Humans Biomarkers, Tumor Microvessels Neoplasm Invasiveness Immunotherapy Machine Learning Risk Assessment Gene Expression Regulation, Neoplastic Liver Liver Neoplasms Precision Medicine Meta-Analysis as Topic Prognosis
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