ArticleNucleic acids research2025
MEBOCOST maps metabolite-mediated intercellular communications using single-cell RNA-seq.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- IGF2-associated tumor cells and APOE-positive macrophages define an imatinib resistance-associated niche in gastrointestinal stromal tumors.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- Deep learning of pretreatment ascites cytopathology for platinum-resistance risk stratification in advanced epithelial ovarian cancer.Neoplasia (New York, N.Y.) · 2026Article
- Article
- hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.Bioinformatics (Oxford, England) · 2026Article
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Vorinostat Potentiates Chemoimmunotherapy in Immune-Enriched Pancreatic Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Gut microbiota-derived metabolites as immune modulators in aging and age-related chronic inflammatory diseases.Ageing research reviews · 2026Review
- Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.Journal of translational medicine · 2026Article
- Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication.Bioinformatics (Oxford, England) · 2026Article
- Digital twins for in vivo metabolic flux estimations in patients with brain cancer.Cell metabolism · 2026Article
- Deciphering immune-inflammatory dysregulation in the endometriotic microenvironment: insights from single-cell omics and artificial intelligence.Frontiers in immunology · 2026Review
- S100A8Frontiers in immunology · 2026Article
- Peripheral γδ T-cell remodeling in psoriasis is associated with effector-biased transcriptional organization and reduced representation of a circulatingFrontiers in immunology · 2026Article
- The High-Altitude Adaptation Characteristics of Microbiota-Host Cross-Talk in Yak Gastrointestinal Track.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The Role of Metabolites in Cell-Cell Communication: A Review of Databases and Computational Tools.Cells · 2025Review
- hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.bioRxiv : the preprint server for biology · 2025Article
- Beyond Bulk Metabolomics: Emerging Technologies for Defining Cell-Type Specific Metabolic Pathways in Health and Disease.Biomolecules · 2025Review
- MetaLigand provides a prior-knowledge-guided framework for predicting non-peptide ligand mediated cell-cell communication.Cell reports methods · 2025Article
- Single-Cell Analysis Reveals a Critical Role for Macrophage Epsins in Regulating the Origin of Foam Cells in Atherosclerosis.Arteriosclerosis, thrombosis, and vascular biology · 2025Article
- Connectome-constrained ligand-receptor interaction analysis for understanding brain network communication.Nature communications · 2025Article
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Authors and funding
15 authors.
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Abstract
Cell-cell communication (CCC) is crucial for cellular function and tissue homeostasis. Existing methods for protein-oriented CCC detection often overlook metabolite-mediated CCC (mCCC), and adapting them to mCCC analysis is challenging due to fundamental differences in the underlying biological mechanisms. To fill this gap, we developed MEBOCOST, an algorithm built on scRNA-seq and metabolic flux balance analysis to detect mCCC among single cells. Comprehensive benchmarking analyses based on simulation, spatial, CRISPR screen, and clinical patient data demonstrated the robustness of MEBOCOST in detecting biologically significant mCCC events. We applied MEBOCOST to scRNA-seq datasets of human white adipose tissues and unraveled macrophages were the predominant source of mCCC reprogramming in obese patients. Moreover, analysis in mice brown adipose tissue successfully recapitulated known and further uncovered new mCCC events, including a glutamine-mediated endothelial-to-adipocyte communication, which was experimentally verified to regulate adipocyte differentiation. Therefore, MEBOCOST is a valuable tool for researchers investigating mCCC in diverse biological contexts and disease samples. MEBOCOST is freely available at https://github.com/kaifuchenlab/MEBOCOST.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.