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Single-Cell Gene Expression Analysis

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Deciphering the role of metal ion transport-related genes in T2D pathogenesis and immune cell infiltration via scRNA-seq and machine learning.

Frontiers in immunology 39926598
INTRODUCTION: Type 2 diabetes (T2D) is a complex metabolic disorder with significant global health implications. Understanding the molecular mechanisms underlying T2D is crucial for developing effective therapeutic strategies. This study employs sing...
Diabetes Mellitus, Type 2 Gene Expression Profiling Gene Regulatory Networks Humans Ion Transport Machine Learning Metals Protein Interaction Maps RNA-Seq Single-Cell Analysis Single-Cell Gene Expression Analysis
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Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks.

Briefings in bioinformatics 39800872
Single-cell multi-omics techniques, which enable the simultaneous measurement of multiple modalities such as RNA gene expression and Assay for Transposase-Accessible Chromatin (ATAC) within individual cells, have become a powerful tool for decipherin...
Chromatin Immunoprecipitation Sequencing Computational Biology Gene Regulatory Networks Graph Neural Networks Humans Neural Networks, Computer RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis
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Identification of potential biomarkers in cardiovascular calcification based on bioinformatics combined with single-cell RNA-seq and multiple machine learning analysis.

Cellular signalling 40024421
BACKGROUND: The molecular and genetic mechanisms underlying vascular calcification remain unclear. This study aimed to determine the differences in calcification marker-related gene expression in macrophages.
Animals Biomarkers Computational Biology Humans Machine Learning Mice Protein Interaction Maps RNA-Seq Single-Cell Analysis Single-Cell Gene Expression Analysis Vascular Calcification
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Development of a MVI associated HCC prognostic model through single cell transcriptomic analysis and 101 machine learning algorithms.

Scientific reports 40055377
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...
Biomarkers, Tumor Carcinoma, Hepatocellular Clinical Decision-Making Datasets as Topic Gene Expression Regulation, Neoplastic Humans Immune Checkpoint Proteins Immunotherapy Kaplan-Meier Estimate Liver Liver Neoplasms Machine Learning Meta-Analysis as Topic Microvessels Mutation Neoplasm Invasiveness Precision Medicine Prognosis Risk Assessment Single-Cell Gene Expression Analysis Treatment Outcome
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Investigation of cell development and tissue structure network based on natural Language processing of scRNA-seq data.

Journal of translational medicine 40038714
BACKGROUND: Single-cell multi-omics technologies, particularly single-cell RNA sequencing (scRNA-seq), have revolutionized our understanding of cellular heterogeneity and development by providing insights into gene expression at the single-cell level...
Animals Cell Differentiation Gene Regulatory Networks Humans Natural Language Processing Organ Specificity RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis
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GRLGRN: graph representation-based learning to infer gene regulatory networks from single-cell RNA-seq data.

BMC bioinformatics 40251476
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...
Algorithms Computational Biology Deep Learning Gene Regulatory Networks Humans Machine Learning RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis
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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 40247403
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...
Adipose Tissue Animals Cellular Microenvironment Female Humans Inflammation Machine Learning Macrophages Male Middle Aged Osteoarthritis Rats Rats, Sprague-Dawley RNA-Seq Single-Cell Analysis Single-Cell Gene Expression Analysis Synovial Membrane
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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 40205350
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 ...
Biomarkers, Tumor Carcinogenesis Cell Line, Tumor Cell Proliferation Computational Biology Gene Expression Regulation, Neoplastic Gene Regulatory Networks Humans Lysine Machine Learning Nomograms Prognosis RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis Stomach Neoplasms Vimentin
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scAMZI: attention-based deep autoencoder with zero-inflated layer for clustering scRNA-seq data.

BMC genomics 40197174
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...
Algorithms Autoencoder Cluster Analysis Computational Biology Deep Learning Humans RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis Software
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scMUSCL: multi-source transfer learning for clustering scRNA-seq data.

Bioinformatics (Oxford, England) 40152244
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...
Algorithms Cluster Analysis Humans Machine Learning Neural Networks, Computer RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis Software
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