AIMC Topic: Single-Cell Analysis

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Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer.

BMC bioinformatics Jul 1, 2025
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression by allowing researchers to analyze the transcriptomes of individual cells. This technology provides unprecedented insights into cellular heterogeneity, cellular st...
Sequence Analysis, RNA Molecular Sequence Annotation Single-Cell Analysis RNA-Seq Single-Cell Gene Expression Analysis Humans Machine Learning Algorithms
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Profiling short-term longitudinal severity progression and associated genes in COVID-19 patients using EHR and single-cell analysis.

Scientific reports Jul 1, 2025
Here we propose CovSF, a deep learning model designed to track and forecast short-term severity progression of COVID-19 patients using longitudinal clinical records. The motivation stems from the need for timely medical resource allocation, improved ...
COVID-19 Electronic Health Records Female Male Middle Aged Deep Learning Disease Progression Humans Single-Cell Analysis SARS-CoV-2 Severity of Illness Index Longitudinal Studies Aged Transcriptome
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Leveraging autoencoder models and data augmentation to uncover transcriptomic diversity of gingival keratinocytes in single cell analysis.

Scientific reports Jul 1, 2025
Periodontitis, a chronic inflammatory condition of the periodontium, is associated with over 60 systemic diseases. Despite advancements, precision medicine approaches have had limited success, emphasizing the need for deeper insights into cellular su...
Gingiva Autoencoder Algorithms Gene Expression Profiling Principal Component Analysis Transcriptome Humans Single-Cell Analysis Keratinocytes Sequence Analysis, RNA
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Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer.

Nature communications Jul 1, 2025
Investigating the temporal dynamics of gene expression is crucial for understanding gene regulation across various biological processes. Using the Fluorescent Timer protein, the Timer-of-cell-kinetics-and-activity system enables analysis of transcrip...
Genes, Reporter Spleen Transcription, Genetic Enhancer Elements, Genetic Mice Mice, Inbred C57BL CRISPR-Cas Systems T-Lymphocytes, Regulatory Gene Expression Regulation Flow Cytometry Forkhead Transcription Factors Machine Learning Animals Single-Cell Analysis Neural Networks, Computer
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Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.

Nature communications Jul 1, 2025
During cell-cell communication (CCC), pathways activated by different ligand-receptor pairs may have crosstalk with each other. While multiple methods have been developed to infer CCC networks and their downstream response using single-cell RNA-seq d...
Humans Machine Learning Gene Expression Profiling Gene Regulatory Networks Signal Transduction Transcription Factors Cell Communication Transcriptome Single-Cell Analysis RNA-Seq
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Identification of pyroptosis related genes and subtypes in atherosclerosis using multiomic and single cell analysis.

Scientific reports Jul 1, 2025
Atherosclerosis (AS), the leading cause of cardiovascular diseases, is a chronic inflammatory disorder involving lipid metabolism, immune dysregulation, and cell death. Pyroptosis, a form of inflammatory programmed cell death, is implicated in AS pro...
Receptors, Immunologic Male Gene Expression Profiling Protein Interaction Maps Transcriptome Mice Single-Cell Analysis Monocytes Humans Pyroptosis Membrane Glycoproteins Macrophages Lipid Metabolism Animals Atherosclerosis
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Prognostic model of lung adenocarcinoma from the perspective of cancer-associated fibroblasts using single-cell and bulk RNA-sequencing.

Scientific reports Jul 1, 2025
Cancer-associated fibroblasts (CAFs) play important roles in the progression of lung adenocarcinoma (LUAD). We examined CAF subgroups via gene ontology, pseudo-time, and cell communication analyses and explored their prognostic value in LUAD using a ...
Prognosis Female Humans Cancer-Associated Fibroblasts Cell Proliferation Cell Movement Biomarkers, Tumor Lung Neoplasms Adenocarcinoma of Lung Sequence Analysis, RNA Gene Expression Regulation, Neoplastic Single-Cell Analysis Machine Learning
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Identification of key genes and development of an identifying machine learning model for sepsis.

Inflammation research : official journal of the European Histamine Research Society ... [et al.] Jun 30, 2025
OBJECTIVE AND DESIGN: This study aims to identify key genes of sepsis and construct a model for sepsis identification through integrated multi-organ single-cell RNA sequencing (scRNA-seq) and machine learning.
Lung Gene Expression Profiling Sepsis Databases, Genetic Single-Cell Analysis Humans Mice Machine Learning Sequence Analysis, RNA Animals Support Vector Machine
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Exploring the relationship between graft dysfunction with serum metabolites and inflammatory proteins: integrating Mendelian randomization, single-cell analysis, machine learning, and SHAP methods for comprehensive analysis.

Renal failure Jun 25, 2025
BACKGROUND: The exact mechanism of graft dysfunction has not been fully clarified. We aimed to explore the causal effects of serum metabolites on graft dysfunction and the mediating role of inflammatory proteins.
Mendelian Randomization Analysis Humans Male Graft Rejection Single-Cell Analysis Kidney Transplantation Machine Learning Biomarkers Female
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CellMemory: hierarchical interpretation of out-of-distribution cells using bottlenecked transformer.

Genome biology Jun 23, 2025
Machine learning methods, especially Transformer architectures, have been widely employed in single-cell omics studies. However, interpretability and accurate representation of out-of-distribution (OOD) cells remains challenging. Inspired by the glob...
Humans Single-Cell Analysis Machine Learning Transcriptome
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