AIMC Topic: Single-Cell Gene Expression Analysis

Clear Filters Showing 41 to 50 of 58 articles

Machine learning using scRNA-seq Combined with bulk-seq to identify lactylation-related hub genes in carotid arteriosclerosis.

Scientific reports May 22, 2025
Atherosclerosis is a chronic inflammatory disease, this study aims to investigate the immune landscape in carotid atherosclerotic plaque formation and explore diagnostic biomarkers of lactylation-associated genes, so as to gain new insights into unde...
Plaque, Atherosclerotic Carotid Artery Diseases Gene Expression Profiling Transcriptome Single-Cell Analysis Single-Cell Gene Expression Analysis Sequence Analysis, RNA RNA-Seq Gene Regulatory Networks Humans Machine Learning Biomarkers
View on PubMed DOI

Scmaskgan: masked multi-scale CNN and attention-enhanced GAN for scRNA-seq dropout imputation.

BMC bioinformatics May 20, 2025
Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but dropout events, where gene expression is undetected in individual cells, present a significant challenge. We propose scMASKGAN, which transforms ma...
Software Algorithms Single-Cell Analysis RNA-Seq Humans Neural Networks, Computer Single-Cell Gene Expression Analysis Sequence Analysis, RNA Neuroblastoma
View on PubMed DOI

scMUSCL: multi-source transfer learning for clustering scRNA-seq data.

Bioinformatics (Oxford, England) May 6, 2025
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...
RNA-Seq Single-Cell Gene Expression Analysis Sequence Analysis, RNA Software Algorithms Single-Cell Analysis Cluster Analysis Humans Neural Networks, Computer Machine Learning
View on PubMed DOI

Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering.

Briefings in bioinformatics May 1, 2025
Clustering is pivotal in deciphering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data. However, it suffers from several challenges in handling the high dimensionality and complexity of scRNA-seq data. Especially when employing gr...
Neural Networks, Computer Machine Learning Algorithms Humans Single-Cell Gene Expression Analysis Animals Computational Biology Single-Cell Analysis Sequence Analysis, RNA RNA-Seq Cluster Analysis
View on PubMed DOI

CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data.

Cell genomics Jan 8, 2025
Exploratory analysis of single-cell RNA sequencing (scRNA-seq) typically relies on hard clustering over two-dimensional projections like uniform manifold approximation and projection (UMAP). However, such methods can severely distort the data and hav...
Mice Sequence Analysis, RNA Unsupervised Machine Learning Single-Cell Analysis RNA-Seq Single-Cell Gene Expression Analysis Brain Animals Gene Expression Profiling Humans
View on PubMed DOI

Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks.

Briefings in bioinformatics Nov 22, 2024
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...
RNA-Seq Gene Regulatory Networks Single-Cell Gene Expression Analysis Chromatin Immunoprecipitation Sequencing Graph Neural Networks Computational Biology Sequence Analysis, RNA Humans Neural Networks, Computer Single-Cell Analysis
View on PubMed DOI

scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning.

Briefings in bioinformatics Nov 22, 2024
Cell type annotation is a critical step in analyzing single-cell RNA sequencing (scRNA-seq) data. A large number of deep learning (DL)-based methods have been proposed to annotate cell types of scRNA-seq data and have achieved impressive results. How...
Single-Cell Analysis RNA-Seq Single-Cell Gene Expression Analysis Sequence Analysis, RNA Mice Computational Biology Algorithms Animals Humans Deep Learning Neural Networks, Computer Software
View on PubMed DOI

Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data.

Briefings in bioinformatics Sep 23, 2024
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for elucidating cellular heterogeneity and tissue function in various biological contexts. However, the sparsity in scRNA-seq data limits the accuracy of cell type annotation and transcriptomi...
Computational Biology Humans Single-Cell Analysis Sequence Analysis, RNA RNA-Seq Algorithms Supervised Machine Learning Gene Expression Profiling Single-Cell Gene Expression Analysis
View on PubMed DOI

scDTL: enhancing single-cell RNA-seq imputation through deep transfer learning with bulk cell information.

Briefings in bioinformatics Sep 23, 2024
The increasing single-cell RNA sequencing (scRNA-seq) data enable researchers to explore cellular heterogeneity and gene expression profiles, offering a high-resolution view of the transcriptome at the single-cell level. However, the dropout events, ...
RNA-Seq Single-Cell Gene Expression Analysis Computational Biology Transcriptome Deep Learning Single-Cell Analysis Sequence Analysis, RNA Humans Algorithms Gene Expression Profiling
View on PubMed DOI

Structure-preserved integration of scRNA-seq data using heterogeneous graph neural network.

Briefings in bioinformatics Sep 23, 2024
The integration of single-cell RNA sequencing (scRNA-seq) data from multiple experimental batches enables more comprehensive characterizations of cell states. Given that existing methods disregard the structural information between cells and genes, w...
Single-Cell Gene Expression Analysis Algorithms Humans Computational Biology Animals Single-Cell Analysis Sequence Analysis, RNA Neural Networks, Computer RNA-Seq
View on PubMed DOI
Popular Topics
Recent Journals