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Single-Cell Analysis

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scRSSL: Residual semi-supervised learning with deep generative models to automatically identify cell types.

IET systems biology 40261690
Single-cell sequencing (scRNA-seq) allows researchers to study cellular heterogeneity in individual cells. In single-cell transcriptomics analysis, identifying the cell type of individual cells is a key task. At present, single-cell datasets often fa...
Computational Biology Deep Learning Humans Neural Networks, Computer Single-Cell Analysis Supervised Machine Learning
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adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks.

Bioinformatics (Oxford, England) 40234247
MOTIVATION: Several machine learning (ML) algorithms dedicated to the detection of healthy and diseased cell types from single-cell RNA sequencing (scRNA-seq) data have been proposed for biomedical purposes. This raises concerns about their vulnerabi...
Algorithms Gene Expression Profiling Humans Machine Learning Sequence Analysis, RNA Single-Cell Analysis Transcriptome
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A multi-view graph convolutional network framework based on adaptive adjacency matrix and multi-strategy fusion mechanism for identifying spatial domains.

Bioinformatics (Oxford, England) 40233119
MOTIVATION: Spatial transcriptomics (ST) addresses the loss of spatial context in single-cell RNA-sequencing by simultaneously capturing gene expression and spatial location information. A critical task of ST is the identification of spatial domains....
Algorithms Computational Biology Gene Expression Profiling Neural Networks, Computer Single-Cell Analysis Software Transcriptome
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FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis.

Briefings in bioinformatics 40211981
Single-cell multi-omics technologies have revolutionized the study of cell states and functions by simultaneously profiling multiple molecular layers within individual cells. However, existing methods for integrating these data struggle to preserve c...
Algorithms Autoencoder Computational Biology Humans Multiomics Neural Networks, Computer Single-Cell Analysis Software
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Study on the mechanism of action of the active ingredient of Calculus Bovis in the treatment of sepsis by integrating single-cell sequencing and machine learning.

Medicine 40258762
BACKGROUND: Sepsis, a complex inflammatory condition with high mortality rates, lacks effective treatments. This study explores the therapeutic mechanisms of Calculus Bovis in sepsis using network pharmacology and RNA sequencing.
China Drugs, Chinese Herbal Humans Machine Learning Molecular Docking Simulation Molecular Dynamics Simulation Network Pharmacology Protein Interaction Maps Sepsis Sequence Analysis, RNA Single-Cell Analysis
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Transfer learning of multicellular organization via single-cell and spatial transcriptomics.

PLoS computational biology 40258090
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...
Animals Computational Biology Drosophila Gene Expression Profiling Humans Machine Learning Mice Neural Networks, Computer Sequence Analysis, RNA Single-Cell Analysis Transcriptome
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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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101 Machine Learning Algorithms for Mining Esophageal Squamous Cell Carcinoma Neoantigen Prognostic Models in Single-Cell Data.

International journal of molecular sciences 40244296
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive malignant tumors in the digestive tract, characterized by a high recurrence rate and inadequate immunotherapy options. We analyzed mutation data of ESCC from public databases and...
Algorithms Antigens, Neoplasm Data Mining Esophageal Neoplasms Esophageal Squamous Cell Carcinoma Humans Machine Learning Mutation Prognosis Single-Cell Analysis Tumor Microenvironment
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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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