Schematic overview of NEP analysis steps (Neighborhood definition, Quantification and NEP score) and the systematic method performance comparison using simulated data for cohort distinction.

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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...

https://www.biorxiv.org/content/10.1101/2024.05.31.596823v2.full

Visualising 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...

Thrilled 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...

Great work with Alexander Theus, David Wissel, and @valboeva.bsky.social.

All of this, while CancerFoundation is trained on much less data and the model is significantly smaller.

The gene embedding learned by CancerFoundation shows grouping of genes by previously discovered Meta-programs.

CancerFoundation's zero-short cell embeddings resemble known transcriptional states established transcriptional states observed in glioblastoma (GBM) and lung adenocarcinoma (LUAD).

CancerFoundation outperformed scFoundation and DeepCDR on drug response prediction.

📢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...

📄 Read the full preprint: biorxiv.org/content/10.1...

Thanks to all co-authors Philip Toma, Imant Daunhawer, Julia Vogt, @flobarkmann.bsky.social, and @valboeva.bsky.social

We are hiring (resharing appreciated)!

Given recent successful grant applications (I got my SNSF Starting Grant 🚀), we are extending the LIAC team with multiple openings (PhD/postdoc) for 2025.

Apply now (deadline: December 20th) by filling in this form: forms.fillout.com/t/eq5ADAw3kkus.
#ChemSky

🚀 New preprint from our lab, Ekaterina Krymova, and @fabiantheis.bsky.social: UniversalEPI, an attention-based method to predict enhancer-promoter interactions from DNA sequence and ATAC-seq🌟 Read the full preprint: www.biorxiv.org/content/10.1... by @aayushgrover.bsky.social, L. Zhang & I.L. Ibarra

🚀 We're #Hiring #PhD students at #MLBio Lab at
@EPFL through the #EDIC Program!
📅 Deadline: Dec 15

💥 We're part of School of Computer Science and School of Life Sciences at EPFL which gives access to excellent collaborators, network, and resources!

👉 Learn more at brbiclab.epfl.ch!