I’ll be talking at the #ISMBECCB2025 about scCellFie and how we can use single-cell and spatial transcriptomics to study metabolism. If you are interested, join the #SysMod COSI on Tue 22th at 5pm (room 01C) 🙌

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

happy to help if you have any question when trying it!

Atlas-scale metabolic activities inferred from single-cell and spatial transcriptomics Metabolism supplies energy, building blocks, and signaling molecules vital for cell function and communication, but methods to directly measure it at single-cell and/or spatial resolutions remain tech...

🔗 Find out more
📄 Preprint: doi.org/10.1101/2025...
💻 GitHub: github.com/earmingol/sc...
📚 Tutorials: sccellfie.readthedocs.io

🤝 Thanks to the Vento Lab and all collaborators!
We hope scCellFie supports your exploration of metabolism in health & disease 🧪
#Metabolism

🧱 In endometrial carcinoma, scCellFie revealed:
• Spatially organized metabolic activities
• Tumor-associated estrogen & kynurenine signaling
• Metabolic tasks linked to tumorigenesis potential
#CancerResearch #SpatialTranscriptomics #SpatialBiology

⚠️ In endometriosis, we found:
• Proinflammatory metabolism in macrophages
• Increased glycolysis & lipid metabolism in epithelial cells
• Shared metabolic shifts in eutopic & ectopic tissues
#Endometriosis #Inflammation

🚺 In the human endometrium, we captured metabolic rewiring across the menstrual cycle — including functions that help with tissue remodeling and managing oxidative stress.
#Endometrium #ReproductiveHealth

🌐 We built a metabolic atlas from ~30 million cells across human organs using @cziscience’s Human Cell Atlas.
Explore it online:
🗺️ www.sccellfie.org
#HumanCellAtlas #SingleCell

🔧 What is scCellFie?
A tool to infer interpretable metabolic insights from single-cell and spatial transcriptomics.
🧰 Key features:
• Metabolic markers
• Condition-specific changes
• Spatial & temporal patterns
• Metabolite-based cell communication

I’m happy to share that our scCellFie manuscript is finally on bioRxiv — a project that was an amazing opportunity to return to my roots in metabolism!
We infer metabolic activity from single-cell & spatial transcriptomics 🧬
Read the pre-print here👇
📄 doi.org/10.1101/2025...