Florian Barkmann
PhD student at Boeva Lab, @ETH_en | Mostly working on ML applied to cancer research | Previously @DKFZ, DKRZ, HKU and university of Tübingen
- Reposted by Florian Barkmann1/ Ever wondered how to best quantify cell-cell neighbor preferences in tissues? We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨ Read more: doi.org/10.1101/2025...
- Reposted by Florian BarkmannVisualising the impact of wounding on cancer cells and the tumor microenvironment at single-cell resolution in situ! Happy to share updated paper with new spatial transcriptomics of human skin tumors using CosMx 6'000-gene panel. All data and code are available. www.biorxiv.org/content/10.1...
- Reposted by Florian BarkmannThrilled to share LUNA🌕 – our new generative AI model that reassembles tissue structures from dissociated cells! LUNA learns spatial priors over existing spatially resolved datasets with the aim to predict cell locations de novo. Check out our paper here: www.biorxiv.org/content/10.1...
- 📢If you are interested in single-cell foundation models (scFMs), stop by our poster (West 109) at the AiDrugX Workshop at Neurips 2024. We will present CancerFoundation, a scFM tailored for studying cancer biology🧬. Preprint: biorxiv.org/content/10.1...
- CancerFoundation outperformed scFoundation and DeepCDR on drug response prediction.
- CancerFoundation's zero-short cell embeddings resemble known transcriptional states established transcriptional states observed in glioblastoma (GBM) and lung adenocarcinoma (LUAD).
-
View full threadGreat work with Alexander Theus, David Wissel, and @valboeva.bsky.social.
