iiinova — where your digital self keeps evolving

Reposted by Florian Barkmann

Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025

1/ 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...

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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Reposted by Florian Barkmann

Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · 24/02/2025

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...

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

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Reposted by Florian Barkmann

Maria Brbic @mariabrbic.bsky.social · 24/02/2025

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...

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Florian Barkmann @flobarkmann.bsky.social · 15/12/2024

📢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...

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Reposted by Florian Barkmann

Olga Ovcharenko @oovcharenko.bsky.social · 12/12/2024

📄 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

biorxiv.org

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Reposted by Florian Barkmann

Philippe Schwaller @pschwllr.bsky.social · 02/12/2024

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

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Reposted by Florian Barkmann

Valentina Boeva @valboeva.bsky.social · 26/11/2024

🚀 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

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Reposted by Florian Barkmann

Maria Brbic @mariabrbic.bsky.social · 25/11/2024

🚀 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!