AIMC Topic: RNA-Seq

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SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution.

BMC bioinformatics Jun 2, 2025
BACKGROUND: Understanding cellular heterogeneity within tissues hinges on knowledge of their spatial context. However, it is still challenging to accurately map cells to their spatial coordinates.
Transcriptome Deep Learning Single-Cell Analysis RNA-Seq Sequence Analysis, RNA Humans Animals Gene Expression Profiling
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Error Reduction in Leukemia Machine Learning Classification With Conformal Prediction.

JCO clinical cancer informatics May 28, 2025
PURPOSE: Recent advances in machine learning have led to the development of classifiers that predict molecular subtypes of acute lymphoblastic leukemia (ALL) using RNA-sequencing (RNA-seq) data. Although these models have shown promising results, the...
Precursor Cell Lymphoblastic Leukemia-Lymphoma Biomarkers, Tumor RNA-Seq Computational Biology Humans Machine Learning
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Identification of mitophagy-related biomarkers in severe acute pancreatitis: integration of WGCNA, machine learning algorithms and scRNA-seq.

Frontiers in immunology May 28, 2025
BACKGROUND: Mitophagy is a highly conserved cellular process in eukaryotic cells that selectively clears dysfunctional or damaged mitochondria through autophagy mechanisms to maintain mitochondrial homeostasis. However, the role of mitophagy in the p...
Biomarkers Animals Gene Expression Profiling Single-Cell Analysis Humans Machine Learning Algorithms Mitophagy Mice Computational Biology Disease Models, Animal Pancreatitis RNA-Seq Gene Regulatory Networks Single-Cell Gene Expression Analysis
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scE2EGAE: enhancing single-cell RNA-Seq data analysis through an end-to-end cell-graph-learnable graph autoencoder with differentiable edge sampling.

Biology direct May 27, 2025
BACKGROUND: Single-cell RNA sequencing (scRNA-Seq) technology reveals biological processes and molecular-level genomic information among individual cells. Numerous computational methods, including methods based on graph neural networks (GNNs), have b...
RNA-Seq Single-Cell Gene Expression Analysis Sequence Analysis, RNA Autoencoder Software Algorithms Single-Cell Analysis Humans Neural Networks, Computer
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Integrative Analysis of Lactylation-Associated Features in Abdominal Aortic Aneurysm and Its Immune Microenvironment Utilizing scRNA-seq and Bulk RNA Sequencing.

Circulation journal : official journal of the Japanese Circulation Society Apr 29, 2025
BACKGROUND: Abdominal aortic aneurysm (AAA) is a vascular disease strongly associated with immune dysregulation and metabolic disturbances. Although lactate metabolism and its associated process, lactylation, have been implicated in various diseases,...
Humans Female Aged Animals Single-Cell Gene Expression Analysis Mice Sequence Analysis, RNA Aortic Aneurysm, Abdominal Male Single-Cell Analysis RNA-Seq
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ScAGCN: Graph Convolutional Network with Adaptive Aggregation Mechanism for scRNA-seq Data Dimensionality Reduction.

Interdisciplinary sciences, computational life sciences Apr 25, 2025
With the development of single-cell RNA-sequencing (scRNA-seq) technology, scRNA-seq data analysis suffers huge challenges due to large scale, high dimensionality, high noise, and high sparsity. To achieve accurately embedded representation in the la...
Computational Biology Humans Sequence Analysis, RNA Neural Networks, Computer Dimensionality Reduction Algorithms Single-Cell Analysis RNA-Seq Single-Cell Gene Expression Analysis
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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...
Deep Learning Single-Cell Gene Expression Analysis Humans Single-Cell Analysis Machine Learning Computational Biology RNA-Seq Sequence Analysis, RNA Algorithms Gene Regulatory Networks
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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 Apr 17, 2025
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...
Single-Cell Analysis RNA-Seq Humans Single-Cell Gene Expression Analysis Machine Learning Rats Animals Macrophages Male Female Middle Aged Adipose Tissue Inflammation Osteoarthritis Synovial Membrane Cellular Microenvironment Rats, Sprague-Dawley
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Assessing concordance between RNA-Seq and NanoString technologies in Ebola-infected nonhuman primates using machine learning.

BMC genomics Apr 10, 2025
This study evaluates the concordance between RNA sequencing (RNA-Seq) and NanoString technologies for gene expression analysis in non-human primates (NHPs) infected with Ebola virus (EBOV). A detailed comparison of both platforms revealed a strong co...
2',5'-Oligoadenylate Synthetase Dendritic Cells RNA-Seq Ebolavirus Hemorrhagic Fever, Ebola Machine Learning Humans Animals Gene Expression Profiling
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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 ...
Humans Machine Learning Prognosis Stomach Neoplasms Biomarkers, Tumor Cell Line, Tumor Nomograms Cell Proliferation Single-Cell Gene Expression Analysis Vimentin Single-Cell Analysis Carcinogenesis Computational Biology Sequence Analysis, RNA RNA-Seq Gene Expression Regulation, Neoplastic Lysine Gene Regulatory Networks
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