AIMC Topic: Single-Cell Gene Expression Analysis

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scSemiPLC: a semi-supervised learning framework for annotating single-cell RNA-Seq data by generating pseudo-labels through clustering.

mSystems Dec 8, 2025
UNLABELLED: Single-cell RNA sequencing (scRNA-seq) technology enables researchers to explore heterogeneity of diverse cell types within complex tissues at the single-cell resolution. Cell annotation, as a crucial step in scRNA-seq data analysis, prov...
Humans Algorithms Single-Cell Gene Expression Analysis Sequence Analysis, RNA Cluster Analysis Supervised Machine Learning Animals Single-Cell Analysis RNA-Seq
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Denoising single-cell RNA-seq data with a deep learning-embedded statistical framework.

BMC bioinformatics Nov 19, 2025
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) provides extensive opportunities to explore cellular heterogeneity but is often limited by substantial technical noise and variability. The prevalence of zero counts, arising from both biological var...
Sequence Analysis, RNA RNA-Seq Single-Cell Gene Expression Analysis Mice Humans Deep Learning Algorithms Animals Single-Cell Analysis
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Deciphering lactate/lactylation networks in AML: integrated scRNA-seq and transcriptomics reveal functions and prognostic model.

BMC cancer Oct 25, 2025
Acute myeloid leukemia (AML) exhibits pronounced heterogeneity, necessitating deep molecular characterization for precision therapy. Lactate metabolism and histone lactylation, influencing tumor biology via epigenetic regulation and immune microenvir...
RNA-Seq Single-Cell Gene Expression Analysis Lactic Acid Gene Expression Profiling Transcriptome Single-Cell Analysis Humans Prognosis Female Biomarkers, Tumor Leukemia, Myeloid, Acute Male
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Single-cell RNA-seq combined with bulk RNA-seq analysis identifies necroptosis-related genes as therapeutic targets for periodontitis.

BMC medical genomics Oct 14, 2025
BACKGROUND: Necroptosis, a regulated form of programmed cell death, exacerbates inflammatory responses by releasing damage-associated molecular patterns and inflammatory factors. However, the specific mechanisms underlying necroptosis in periodontiti...
Sequence Analysis, RNA Necroptosis Periodontitis Single-Cell Analysis RNA-Seq Single-Cell Gene Expression Analysis Humans Gene Expression Profiling
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Paired snRNA-seq and scRNA-seq analysis of MASLD patients to identify early-stage markers for disease progression.

Hepatology communications Oct 7, 2025
BACKGROUND AND AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of chronic liver disease worldwide. Progression from simple metabolic dysfunction-associated steatotic liver (MASL) without necro-inflammation to...
Humans Biomarkers Male Middle Aged Female Adult Single-Cell Gene Expression Analysis Leukocytes, Mononuclear Transcriptome Fatty Liver Liver Cirrhosis Disease Progression Single-Cell Analysis Liver Gene Expression Profiling RNA-Seq Sequence Analysis, RNA
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Integrative analysis of scRNA-seq and bulk RNA-seq to identify lactylation-related gene signatures in lung ischemia-reperfusion injury after lung transplantation.

International immunopharmacology Sep 5, 2025
BACKGROUND: Protein lactylation has been implicated in stress-responsive cellular mechanisms, yet its role in lung transplantation-associated ischemia-reperfusion injury (IRI) remains undefined.
Animals Male Lung Gene Expression Profiling Humans Machine Learning Biomarkers Reperfusion Injury Lung Transplantation Transcriptome Single-Cell Gene Expression Analysis Single-Cell Analysis RNA-Seq Mice Mice, Inbred C57BL
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Machine learning integration of bulk and single-cell RNA-seq data reveals glycolytic heterogeneity in colorectal cancer.

Medical oncology (Northwood, London, England) Aug 30, 2025
As one of the most prevalent malignancies worldwide, colorectal cancer (CRC) exhibits a strong metabolic dependency on glycolysis, which fuels tumor expansion and shapes an immunosuppressive microenvironment. Despite its clinical significance, the re...
Glycolysis Single-Cell Analysis Machine Learning RNA-Seq Single-Cell Gene Expression Analysis Humans Colorectal Neoplasms Tumor Microenvironment
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CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

BMC biology Jul 30, 2025
BACKGROUND: The advent of single-cell RNA sequencing (scRNA-seq) has provided unprecedented insights into cancer cellular diversity, enabling a comprehensive understanding of cancer at the single-cell level. However, identifying cancer cells remains ...
Humans Machine Learning RNA-Seq Single-Cell Gene Expression Analysis Sequence Analysis, RNA Neoplasms Transcriptome 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...
Molecular Sequence Annotation Humans RNA-Seq Machine Learning Single-Cell Gene Expression Analysis Algorithms Sequence Analysis, RNA Single-Cell Analysis
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scGANSL: Graph Attention Network with Subspace Learning for scRNA-seq Data Clustering.

Journal of chemical information and modeling Jun 5, 2025
Single-cell RNA sequencing (scRNA-seq) has become a crucial technology for analyzing cellular diversity at the single-cell level. Cell clustering is crucial in scRNA-seq data analysis as it accurately identifies distinct cell types and uncovers poten...
Cluster Analysis Principal Component Analysis Humans RNA-Seq Machine Learning Single-Cell Analysis Single-Cell Gene Expression Analysis Sequence Analysis, RNA
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