AIMC Topic: Sequence Analysis, RNA

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Circular RNA discovery with emerging sequencing and deep learning technologies.

Nature genetics Apr 17, 2025
Circular RNA (circRNA) represents a type of RNA molecule characterized by a closed-loop structure that is distinct from linear RNA counterparts. Recent studies have revealed the emerging role of these circular transcripts in gene regulation and disea...
Sequence Analysis, RNA High-Throughput Nucleotide Sequencing RNA, Circular Animals Deep Learning Single-Cell Analysis Artificial Intelligence Algorithms Humans
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Integrating Machine Learning and Bulk and Single-Cell RNA Sequencing to Decipher Diverse Cell Death Patterns for Predicting the Prognosis of Neoadjuvant Chemotherapy in Breast Cancer.

International journal of molecular sciences Apr 13, 2025
Breast cancer (BRCA) continues to pose a serious risk to women's health worldwide. Neoadjuvant chemotherapy (NAC) is a critical treatment strategy. Nevertheless, the heterogeneity in treatment outcomes necessitates the identification of reliable biom...
Breast Neoplasms Biomarkers, Tumor Middle Aged Gene Expression Regulation, Neoplastic Single-Cell Analysis Humans Machine Learning Neoadjuvant Therapy Cell Death Sequence Analysis, RNA Prognosis Female
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Identification of novel metabolism-related biomarkers of Kawasaki disease by integrating single-cell RNA sequencing analysis and machine learning algorithms.

Frontiers in immunology Apr 10, 2025
BACKGROUND: The bile acid metabolism (BAM) and fatty acid metabolism (FAM) have been implicated in Kawasaki disease (KD), but their precise mechanisms remain unclear. Identifying signature cells and genes related to BAM and FAM could offer a deeper u...
Monocytes Gene Expression Profiling Sequence Analysis, RNA Transcriptome Fatty Acids Humans Single-Cell Analysis Mucocutaneous Lymph Node Syndrome Machine Learning Biomarkers
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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 ...
Single-Cell Analysis RNA-Seq Gene Regulatory Networks Sequence Analysis, RNA Prognosis Vimentin Humans Nomograms Biomarkers, Tumor Gene Expression Regulation, Neoplastic Cell Line, Tumor Single-Cell Gene Expression Analysis Stomach Neoplasms Cell Proliferation Lysine Computational Biology Carcinogenesis Machine Learning
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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...
Sequence Analysis, RNA Cluster Analysis Autoencoder Software Algorithms Deep Learning Humans Single-Cell Gene Expression Analysis Computational Biology Single-Cell Analysis RNA-Seq
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Large-scale bulk and single-cell RNA sequencing combined with machine learning reveals glioblastoma-associated neutrophil heterogeneity and establishes a VEGFA neutrophil prognostic model.

Biology direct Apr 5, 2025
BACKGROUND: Neutrophils play a key role in the tumor microenvironment (TME); however, their functions in glioblastoma (GBM) are overlooked and insufficiently studied. A detailed analysis of GBM-associated neutrophil (GBMAN) subpopulations may offer n...
Humans Machine Learning Prognosis Tumor Microenvironment Neutrophils Glioblastoma Vascular Endothelial Growth Factor A Brain Neoplasms Single-Cell Analysis Sequence Analysis, RNA
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Integrating single-cell RNA sequencing, WGCNA, and machine learning to identify key biomarkers in hepatocellular carcinoma.

Scientific reports Apr 1, 2025
The microarray and single-cell RNA-sequencing (scRNA-seq) datasets of hepatocellular carcinoma (HCC) were downloaded from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (W...
Humans Single-Cell Analysis Gene Regulatory Networks Sequence Analysis, RNA Gene Expression Regulation, Neoplastic Machine Learning Gene Expression Profiling Biomarkers, Tumor Liver Neoplasms Molecular Docking Simulation Carcinoma, Hepatocellular
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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...
Humans RNA-Seq Single-Cell Gene Expression Analysis Sequence Analysis, RNA Chromatin Neural Networks, Computer Algorithms Single-Cell Analysis
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scMalignantFinder distinguishes malignant cells in single-cell and spatial transcriptomics by leveraging cancer signatures.

Communications biology Mar 27, 2025
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for characterizing tumor heterogeneity, yet accurately identifying malignant cells remains challenging. Here, we propose scMalignantFinder, a machine learning tool specifically designed to dis...
Sequence Analysis, RNA Machine Learning Gene Expression Profiling Humans Gene Expression Regulation, Neoplastic Neoplasms Transcriptome Single-Cell Analysis
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Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

PLoS genetics Mar 19, 2025
Deep learning techniques are increasingly utilized to analyze large-scale single-cell RNA sequencing (scRNA-seq) data, offering valuable insights from complex transcriptome datasets. Geneformer, a pre-trained model using a Transformer Encoder archite...
Sequence Analysis, RNA Species Specificity Humans Deep Learning Single-Cell Analysis RNA-Seq Animals Gene Expression Profiling Mice Transcriptome
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