Omer Ali Bayraktar

Group leader at @sangerinstitute Neural diversity, spatial transcriptomics, glia, GBM

[Omer Ali Bayraktar @bayraktar_lab]

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! https://t.co/2GIBjLMz0w

[Tanzila Mukhtar- Warrior @tmturkee]

In our new preprint, we mapped Broca’s area & motor cortex across human development using single-nucleus multiome + Xenium spatial transcriptomics. Huge congrats to the team! https://t.co/JaysSksAPs
@ChanZuckerberg @bayraktar_lab @LabNowakowski
@Kriegsteinlab @UCSFstemcell

[Mo Lotfollahi @mo_lotfollahi]

🧬✨ How can we generate genome-wide gene expression in 3D to build 3D virtual organs—without performing spatial transcriptomics on every single tissue section?

Today, most spatial transcriptomics is still 2D 🧫: we capture one thin slice at a time. But real biology—development, disease niches, gradients, and cell–cell communication—unfolds in 3D 🧠🫀. Measuring ST across many serial sections is possible, but it’s still too expensive and labor-intensive 💸⏳ for routine studies.

We introduce HoloTea 🍵, a flow-matching–based generative AI approach 🤖 that learns from dense serial H&E histology stacks 🧾 plus ST measured on only a subset of slices, then reconstructs the missing slices to produce a 3D-consistent volumetric spatial transcriptomics readout 📍📈🧬.

Across multiple datasets (including large serial stacks), HoloTea improves reconstruction accuracy ✅ compared to strong 2D and 3D baselines, while remaining scalable 🚀 to large tissue volumes.

We see this as a step toward accurate 3D virtual tissues 🌍🧫—enabling cheaper volumetric molecular maps 💡, faster biomarker discovery 🔍, and deeper insight into 3D tissue organization in health and disease 🏥.

📄 Paper: https://t.co/BOzrQ3bpox
🤝 Amazing collaboration with @Muzz_Haniffa @bayraktar_lab @Lastu21 led by @ArshiaHemmat @AmirhVahidi Mohammad Vali Sanian

#SpatialTranscriptomics #BioAI #GenAI #DigitalPathology #3DBiology

[Omer Ali Bayraktar @bayraktar_lab]

@soyonhonglab congrats!

[Hilary Martin @hilsomartin]

Happy to have helped with this great project on expression patterns of autism-associated genes in developing brain, led by @bayraktar_lab, showing surprising enrichment in the thalamus. https://t.co/HYfruOfej7... Genetics analyses in @SPARKforAutism by @mahmoudkokomusa.

[Omer Ali Bayraktar @bayraktar_lab]

Grateful to @hilsomartin, Tom Nowakowski and many other authors (which I could not @ because the auto suggests here are now terrible!)

[Omer Ali Bayraktar @bayraktar_lab]

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! https://t.co/2GIBjLMz0w

[Omer Ali Bayraktar @bayraktar_lab]

3) Our work suggests thalamocortical circuit development is a major hub of autism susceptibility & organoid/animal models of autism need to take this into account

[Omer Ali Bayraktar @bayraktar_lab]

@RongFan8 @Kriegsteinlab @HongyuZhao2 @CJM_lab @peruhlen congrats rong and team!

[Wellcome Sanger Institute @sangerinstitute]

A new dimension of genomics is here. Spatial transcriptomics is transforming how we understand tissues – revealing where genes act, and why it matters. 🧬

Try our spatial-inspired game before reading the latest blog 📷
https://t.co/405vaAC4w3