AIMC Topic: Sequence Analysis, RNA

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Transfer learning of multicellular organization via single-cell and spatial transcriptomics.

PLoS computational biology Apr 21, 2025
Biological tissues exhibit complex gene expression and multicellular patterns that are valuable to dissect. Single-cell RNA sequencing (scRNA-seq) provides full coverages of genes, but lacks spatial information, whereas spatial transcriptomics (ST) m...
Computational Biology Neural Networks, Computer Sequence Analysis, RNA Machine Learning Drosophila Animals Transcriptome Gene Expression Profiling Single-Cell Analysis Humans Mice
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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...
Machine Learning Algorithms Deep Learning Gene Regulatory Networks Single-Cell Gene Expression Analysis Single-Cell Analysis RNA-Seq Humans Computational Biology 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...
Middle Aged Single-Cell Analysis Sequence Analysis, RNA Gene Expression Regulation, Neoplastic Female Breast Neoplasms Machine Learning Humans Biomarkers, Tumor Neoadjuvant Therapy Prognosis Cell Death
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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 Sequence Analysis, RNA Mucocutaneous Lymph Node Syndrome Fatty Acids Humans Gene Expression Profiling Machine Learning Transcriptome Biomarkers Single-Cell Analysis
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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 ...
Carcinogenesis Vimentin Lysine Gene Expression Regulation, Neoplastic Nomograms Cell Proliferation Cell Line, Tumor Single-Cell Analysis RNA-Seq Computational Biology Machine Learning Gene Regulatory Networks Sequence Analysis, RNA Humans Prognosis Stomach Neoplasms Single-Cell Gene Expression Analysis Biomarkers, Tumor
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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...
Autoencoder Computational Biology Sequence Analysis, RNA Cluster Analysis Humans Software Algorithms RNA-Seq Single-Cell Gene Expression Analysis Deep Learning Single-Cell Analysis
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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 Sequence Analysis, RNA Neutrophils Glioblastoma Vascular Endothelial Growth Factor A Tumor Microenvironment Brain Neoplasms Single-Cell Analysis
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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...
Single-Cell Analysis Gene Regulatory Networks Molecular Docking Simulation Sequence Analysis, RNA Gene Expression Profiling Liver Neoplasms Humans Gene Expression Regulation, Neoplastic Carcinoma, Hepatocellular Machine Learning Biomarkers, Tumor
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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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