AIMC Topic: Single-Cell Analysis
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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...
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...
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...
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 ...
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.
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.
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...
WISP2/CCN5 revealed as a potential diagnostic biomarker for endometriosis based on machine learning and single-cell transcriptomic analysis.
Functional & integrative genomics
Jun 19, 2025
OBJECTIVE: Endometriosis is a prevalent gynecological disease characterized by the ectopic growth of functional endometrial tissue outside the uterine cavity, affecting millions of women worldwide. Currently, the definitive diagnosis relies on invasi...
Neurodegeneration Promotes Tumorigenesis in Colorectal Cancer: Insights From Single-Cell and Spatial Multiomics.
JCO precision oncology
Jun 6, 2025
PURPOSE: Colorectal cancer (CRC) ranks third in global incidence and second in mortality, with rates increasing among younger populations. The enteric nervous system (ENS) is crucial for gastrointestinal function, and its dysfunction is associated wi...
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...
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