AIMC Topic: Cell Communication
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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...
Prediction of Ligand-Receptor Interactions Based on CatBoost and Deep Forest and Their Application in Cell-Cell Communication Analysis.
Journal of chemical information and modeling
May 30, 2025
Cell-to-cell communication (CCC) is prominent for cell growth and development as well as tissue and organ formation. CCC inference can help us to deeply understand cellular interplay and discover potential therapeutic targets for complex diseases. Ce...
SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data.
Nature communications
Mar 27, 2025
Spatial omics technologies enable analysis of gene expression and interaction dynamics in relation to tissue structure and function. However, existing computational methods may not properly distinguish cellular intrinsic variability and intercellular...
Spatially Informed Graph Structure Learning Extracts Insights from Spatial Transcriptomics.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Oct 9, 2024
Embeddings derived from cell graphs hold significant potential for exploring spatial transcriptomics (ST) datasets. Nevertheless, existing methodologies rely on a graph structure defined by spatial proximity, which inadequately represents the diversi...
Collection of microrobots for gentle cell manipulation.
Science robotics
Aug 28, 2024
Optically actuated soft microrobotic tools were designed for cell transportation, manipulation, and cell-to-cell interactions.
A novel CAF-cancer cell crosstalk-related gene prognostic index based on machine learning: prognostic significance and prediction of therapeutic response in head and neck squamous cell carcinoma.
Journal of translational medicine
Jul 9, 2024
BACKGROUND: Cancer-associated fibroblast (CAF)-cancer cell crosstalk (CCCT) plays an important role in tumor microenvironment shaping and immunotherapy response. Current prognostic indexes are insufficient to accurately assess immunotherapy response ...
scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis.
Genome biology
Jun 24, 2024
Spatial transcriptomics has transformed our ability to study tissue complexity. However, it remains challenging to accurately dissect tissue organization at single-cell resolution. Here we introduce scHolography, a machine learning-based method desig...
TENET: Triple-enhancement based graph neural network for cell-cell interaction network reconstruction from spatial transcriptomics.
Journal of molecular biology
Mar 18, 2024
Cellular communication relies on the intricate interplay of signaling molecules, forming the Cell-cell Interaction network (CCI) that coordinates tissue behavior. Researchers have shown the capability of shallow neural networks in reconstructing CCI,...
The critical role of neutrophil-endothelial cell interactions in sepsis: new synergistic approaches employing organ-on-chip, omics, immune cell phenotyping and modeling to identify new therapeutics.
Frontiers in cellular and infection microbiology
Jan 8, 2024
Sepsis is a global health concern accounting for more than 1 in 5 deaths worldwide. Sepsis is now defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Sepsis can develop from bacterial (gram negative or g...
Exploring the advances of single-cell RNA sequencing in thyroid cancer: a narrative review.
Medical oncology (Northwood, London, England)
Dec 21, 2023
Thyroid cancer, a prevalent form of endocrine malignancy, has witnessed a substantial increase in occurrence in recent decades. To gain a comprehensive understanding of thyroid cancer at the single-cell level, this narrative review evaluates the appl...
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