Honoured to have received the Trainee Award for my talk together with @drjimmylee.bsky.social at the International Conference on Genomics and Systems Biology of Human Disease and Aging (@aegeanconf.bsky.social), with strong @bayraktarlab.bsky.social presence to showcase our spatial omics research.

I have an opening for a staff scientist or bioinformatician in my group at the Sanger Institute (closing date 24 March). Our current projects focus on disentangling rare and common variant contributions to rare neurodevelopmental conditions and to neurodevelopmental and perinatal traits. 1/2

Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n

bioRxiv Genomics@biorxiv-genomic.bsky.social · 6mo ago

Mapping trans-eQTLs at single-cell resolution using Latent Interaction Variational Inference. https://www.biorxiv.org/content/10.64898/2026.02.04.703363v1

The webinar series on spatial transcriptomics analysis is now open for registration! Join me on 18 March to learn how we at @bayraktarlab.bsky.social integrate single-cell and spatial transcriptomics to map the rules of neurological conditions.

EMBL-EBI Training@training.ebi.embl.org · 6mo ago

We're pleased to announce that our next webinar series is now live. Decoding spatial transcriptomics through sequences, pixels, and bioinformatics will run from 18 February – 8 April 2026: www.ebi.ac.uk/training/eve... Coordinated by: @ajaymishra24.bsky.social, Kristy Ou, and Flaminia Zane. 🧬🖥️📊

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

Omer Ali Bayraktar@bayraktarlab.bsky.social · 9mo ago

Which human brain circuits are implicated in neurodevelopmental conditions? We bridged human genetics, spatial transcriptomics and neurodevelopment to discover the convergence of autism-associated genes in the developing human thalamus! www.biorxiv.org/content/10.1...

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! 🤗

Nature Reviews Genetics@natrevgenet.nature.com · last yr.

Predicting gene expression from DNA sequence using deep learning models go.nature.com/3F8r0Li #Review by Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel & Jeroen de Ridder @nkinl.bsky.social @umcutrecht.bsky.social

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

Wellcome Sanger Institute@sangerinstitute.bsky.social · last yr.

How lung damage worsens during COVID-19 has been mapped at a cellular level. 🦠 By understanding how our lungs respond to the virus over time, this new knowledge may help identify future therapies for COVID-19. www.sanger.ac.uk/news_item/ce...

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.

Wellcome Sanger Institute@sangerinstitute.bsky.social · last yr.

Read ‘Cell2fate infers RNA velocity modules to improve cell fate prediction’ from @sangerinstitute.bsky.social @embl.org and @dkfz.bsky.social in @naturemethods.bsky.social here: bit.ly/3Diarf5

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/

Tomàs Montserrat Ayuso@tmontsay.bsky.social · 2y ago

scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified! 2/8