AIMC Topic: Single-Cell Gene Expression Analysis

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Integrating bulk RNA-seq and scRNA-seq analyses with machine learning to predict platinum response and prognosis in ovarian cancer.

Scientific reports
Platinum-based therapy is an integral part of the standard treatment for ovarian cancer. However, despite extensive research spanning several decades, the identification of dependable predictive biomarkers for platinum response in clinical practice h...

Identification of novel therapeutic targets in hepatitis-B virus-associated membranous nephropathy using scRNA-seq and machine learning.

Scientific reports
Hepatitis B Virus-associated membranous nephropathy (HBV-MN) significantly impacts renal health, particularly in areas with high HBV prevalence. Understanding the molecular mechanisms underlying HBV-MN is crucial for developing effective therapeutic ...

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

Scientific reports
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...

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

BMC bioinformatics
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...

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

Bioinformatics (Oxford, England)
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...

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

Briefings in bioinformatics
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...

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

Cell genomics
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...

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

Briefings in bioinformatics
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...

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

Briefings in bioinformatics
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...

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

Briefings in bioinformatics
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...