Beyond excited to share my first work with Omer's group at Sanger! With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics! 🧵👇 Background / motivation / key results

Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!

Bayraktar, Bassett and Lotfollahi labs are studying how neurodegenerative diseases (ALS, PD, AZ) spatially organise 🧠🧬 Join us to generate & analyse wealths of Xenium data: - Tech specialist: sanger.wd103.myworkdayjobs.com/en-US/Wellco... - AI postdoc: sanger.wd103.myworkdayjobs.com/en-US/Wellco...

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

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 🧵

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...

Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗

Thrilled to share our new @naturecomms.bsky.social study with @sam-n-barnett.bsky.social on early vs late #COVID19 lung damage 🫁. Using single-cell & histopathology-informed #SpatialTranscriptomics, we uncovered key biomarkers & immune patterns. Thanks to collaborators, UKCIC & @humancellatlas.org

Another great computational method out of the Bayraktar lab! Alexander Aivazidis has been a great colleague in our lab and it's amazing to see the capstone of his PhD is now published.

Next weekend I will run the Cambridge half marathon with @sangerinstitute.bsky.social colleagues 🏃‍♂️ Two amazing people are running for charities, please support them!

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/