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) 🙌
21.07.2025 11:36 — 👍 2 🔁 0 💬 1 📌 0
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 🧵
16.05.2025 11:42 — 👍 73 🔁 31 💬 6 📌 5
happy to help if you have any question when trying it!
16.05.2025 06:51 — 👍 0 🔁 0 💬 0 📌 0
🧱 In endometrial carcinoma, scCellFie revealed:
• Spatially organized metabolic activities
• Tumor-associated estrogen & kynurenine signaling
• Metabolic tasks linked to tumorigenesis potential
#CancerResearch #SpatialTranscriptomics #SpatialBiology
15.05.2025 08:21 — 👍 1 🔁 0 💬 1 📌 0
⚠️ In endometriosis, we found:
• Proinflammatory metabolism in macrophages
• Increased glycolysis & lipid metabolism in epithelial cells
• Shared metabolic shifts in eutopic & ectopic tissues
#Endometriosis #Inflammation
15.05.2025 08:21 — 👍 0 🔁 0 💬 1 📌 0
🚺 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
15.05.2025 08:21 — 👍 0 🔁 0 💬 1 📌 0
Metabolic Task Visualizer
🌐 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
15.05.2025 08:21 — 👍 0 🔁 0 💬 1 📌 0
🔧 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
15.05.2025 08:21 — 👍 0 🔁 0 💬 1 📌 0
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...
15.05.2025 08:21 — 👍 6 🔁 1 💬 1 📌 1
Postdoc @broadinstitute.org @harvard.edu #MGH - Immunogenomics - PhD in Genomics🧬 @cam.ac.uk @sangerinstitute.bsky.social🔬 #LCG-UNAM
This is the official twitter account from the Institute of Computational Genomics, RWTH Aachen.
Scientist studying epithelial biology, stem cells and cancer at UCL (@epicentr.bsky.social) 🫁
Postdoctoral fellow at Wellcome Sanger Institute
JDA-certified dermatology consultant
Assistant Professor leading the Computational Biomedicine Group at the University of Innsbruck • Data scientist at the Digital Science Center (DiSC) • Precision medicine and cancer immunotherapy • Mother 🧬🖥️
https://computationalbiomedicinegroup.github.io/
Group leader
@sangerinstitute.bsky.social Neural diversity, spatial transcriptomics, glia, GBM
Postdoc in ML for genomics with Dana Pe'er and Oliver Stegle
Previously at Genentech, UBC and BITS Pilani
https://scholar.google.com/citations?user=4yUtALcAAAAJ&hl=en&oi=ao
Harnessing the power of tissue T cell immunity - Assistant Professor @ La Jolla Institute for Immunology | San Diego | https://www.reinalab.org
Postdoc in Lars Velten's lab @crg.eu, working on gene regulation in haematopoiesis using ML techniques
https://jacobhepkema.github.io
Senior Data Scientist - Bayraktar Group @sangerinstitute.bsky.social
Instagram: Sanger2Helmholtz
🇳🇱 in 🇬🇧 running scripts 🧑💻 and kilometers 🏃
Spatial biology and gene expression research in neurodevelopmental disease @ Bayraktar lab, Wellcome Sanger Institute
Computational biologist using omics data (imaging, gene expression) to investigate the impacts of environmental contaminants on biological systems
Group Leader @EMBL-EBI (www.ewaldlab.org)
Postdoctoral researcher at @anshulkundaje.bsky.social Machine learning #ML, gene regulatory networks #GRN, single cell and spatial #omics.
Previously at @saezlab.bsky.social
Core developer of https://decoupler.readthedocs.io/ at @scverse.bsky.social
He/him. Computational Biologist. Lead multi-omic data analysis and integration with mechanistic prior knowledge in complex diseases @saezlab.bsky.social
Opinions are my own
Scientist at @saezlab.bsky.social, Heidelberg University. EMBL-EBI Visitor. Mathematical modeling / ML & AI for biological systems
https://pablormier.github.io/
Group leader - computational biomedical discovery. Heidelberg University & Heidelberg University Hospital. https://www.tanevskilab.org
computational scientific discovery, biomedicine, spatial omics
PhD student at Wellcome Sanger Institute associated with Haniffa, Parts and Saez-Rodriguez Labs
