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Reposted by Omer Ali Bayraktar

Open Targets @opentargets.org · Jul 3

NEW: Technical specialist with @bayraktarlab.bsky.social

Generate large-scale spatial transcriptomic datasets to create comparative cell atlases of ALS, Alzheimer’s disease and Parkinson’s disease

#scienceJobs #neuroskyence

sanger.wd103.myworkdayjobs.com/en-US/Wellco...

Technical Specialist: Neurodegenerative Disease Spatial Transcriptomics and Data Generation

Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...

sanger.wd103.myworkdayjobs.com

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Reposted by Omer Ali Bayraktar

Open Targets @opentargets.org · Jul 3

NEW: Postdoc in neurodegenerative disease spatial transcriptomics and ML with @bayraktarlab.bsky.social/Mo Lotfollahi

Join a new project to create comparative cell atlases of ALS, Alzheimer’s disease and Parkinson’s disease

#postdocJobs #neuroskyence

sanger.wd103.myworkdayjobs.com/en-US/Wellco...

Postdoctoral Fellow: Neurodegenerative Disease Spatial Transcriptomics and Machine Learning

Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...

sanger.wd103.myworkdayjobs.com

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Reposted by Omer Ali Bayraktar

Jimmy Lee @drjimmylee.bsky.social · Jun 30

📢 @bayraktarlab.bsky.social & colabs at @sangerinstitute.bsky.social are assembling the @opentargets.org funded Neuroimmune Team 🧠🧬-Leverage AI to uncover neurodegeneration

Tech Spec: sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Postdoc AI: sanger.wd103.myworkdayjobs.com/en-US/Wellco...

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 24

Very excited about our new chapter with @mhaniffa.bsky.social !

Muzz Haniffa @mhaniffa.bsky.social · May 23

I am excited to begin my new journey as the Head of Cellular Genomics @sangerinstitute.bsky.social

We will decode and recode tissue ecosystems using AI + big data…

Our amazing faculty include Roser Vento-Tormo, @bayraktarlab.bsky.social, Mo Lotfollahi, Sam Behjati and Song Chen..

Wellcome Sanger Institute @sangerinstitute.bsky.social · May 20

Our newly appointed Head of the Cellular Genomics programme, @mhaniffa.bsky.social, shares her career journey and vision for the future of the programme. Read more below. ⤵️

sangerinstitute.blog/2025/05/20/i...

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 18

Thanks Muzz!

Omer Ali Bayraktar @bayraktarlab.bsky.social · May 18

Thanks Adrien!

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Reposted by Omer Ali Bayraktar

Stein Aerts @steinaerts.bsky.social · May 16

Two massive glioblastoma papers, datasets, trajectories, insights, and.. a very cool new method for GRN inference - scDORI -from @steglelab.bsky.social @oliverstegle.bsky.social @bayraktarlab.bsky.social & Moritz Mall www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics

Glioblastoma (GB) is one of the most lethal human cancers, marked by profound intratumoral heterogeneity and near-universal treatment resistance. Cellular plasticity, the capacity of cancer cells to t...

www.biorxiv.org

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 17

Thanks Chris!

Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Grateful to >60 authors for their amazing work + @wellcomeleap.bsky.social (special thx to Jason Swedlow for leading DeltaT!) & @cziscience.bsky.social for their support. @ebi.embl.org @crick.ac.uk @cambridgeuni.bsky.social @dkfz.bsky.social @sangerinstitute.bsky.social

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Finally, you can access & navigate almost all of our GB single cell and spatial data in our portal @ www.gbmspace.org built with webatlas2 (go.nature.com/4dEr9mN)

GBM-Space: Multi-modal Atlas of Glioblastoma

Explore GBM-Space, a comprehensive cell and tissue Atlas of Glioblastoma combining spatial transcriptomics, single-cell data, and more.

www.gbmspace.org

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

There are many implications & LOTS of detail in the preprints (e.g. mesenchymal cancer states is really a gliosis/hypoxia response & GB tumour subtypes are likely confounded) bit.ly/4mkrWgs bit.ly/3FbI6Ic

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Taken together, these 2 studies start to unveil what i call the “rules” of glioblastoma. Despite their incredible complexity, these tumours are governed by specific cellular & tissue mechanisms. We believe/hope this understanding will be a foundation for new therapies

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

In GB, as opposed to unrestrained plasticity of cancer cells, we predict transition highways and barriers aligned with paper 1. And we mechanistically validate a transcriptional repressor safeguarding neuronal like cancer states!

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

scDORI enables us to examine GRNs in a continuous manner across cellular trajectories. Hence, you don’t just map GRNs / TF regulators, you can actually infer cell plasticity and predict the future state of a given cell

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Here we developed a new deep learning based GRN inference framework: scDORI. See the thread from Manu for more details but few highlights here bsky.app/profile/manu...

Manu Saraswat @manusaraswat.bsky.social · May 16

🧠 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🧵👇

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

In paper 2, we leverage our massive snRNA-ATACseq data to predict cancer cell state transitions & trajectories from gene regulatory networks. Led in @oliverstegle.bsky.social and Moritz Mall's labs by @manusaraswat.bsky.social @lauraruedag.bsky.social Elisa + Tannia & Fani

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

This picture is very consistent with a concurrent study from @sten.linnarsson.org - check their paper out: www.biorxiv.org/content/10.1...

Futile wound healing drives mesenchymal-like cell phenotypes in human glioblastoma

Glioblastoma is the deadliest brain cancer, characterized by large cellular diversity whose complexity and organizing principles are only starting to be uncovered. Both neurodevelopment-like and mesen...

www.biorxiv.org

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Hence, we define a stereotyped trajectory of cancer cells at the heart of GB heterogeneity - unifying previously defined cell states & tumour subtypes

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Finally, cancer cells are not riding alone. We found that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments.

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

This led to a wonderful side quest: we mapped tumour subclones in space! We developed SpaceTree to deconvolve tumour subclones in Visium data and found that they are finely spatially intermixed (within Visium spots) in the tissue! github.com/PMBio/spaceT...

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

These results suggest that this trajectory cuts across the genetic hierarchy of GB i.e. shared across tumours/subclones. We used spatial DNA-seq (LCM-WGS) to validate this +found the trajectory is shared, yet genetically malleable.

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Unbiased transcriptomic trajectory analysis (i.e. our cell2fate RNA velocity go.nature.com/4km62aI) finds that this is trajectory shared across tumours + genetic subclones. And we define a molecular progression conserved across tumours/clones

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

When you look into the tumour areas/states dominated by gliosis/hypoxia, these transitions become clear. You can see cancer cells travelling from developmental astrocyte like states gradually into gliosis + hypoxia response (more on this below)

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

..to resolving this trajectory. Integrating single nuclei + spatial data revealed stepwise spatial transitions of cancer cell states from the tumour invasive edge towards the necrotic core. This looked like spatially organised cancer cell transitions as GB tumours rapidly expand.

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Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

It started with single nuclei RNA-seq. Profiling >1 million cells, we saw within each tumour that cancer cells vary from developmental progenitor-like states (e.g.NPC/OPC) to those marked by gliosis (i.e. glial injury response) & hypoxia Yet, the spatial/tissue context was the key…

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