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Reposted by Cenk Celik

Maria Secrier @mariasecrier.bsky.social · 3d

How do tissues organise, adapt, or collapse? 🧬
We’re looking for a postdoc with strong quantitative skills to tackle these questions in a highly interdisciplinary project bridging spatial omics, ecology & mathematical modelling (expertise required in at least one topic).
Apply 👉 tinyurl.com/3d37d3st

UCL – University College London

UCL is consistently ranked as one of the top ten universities in the world (QS World University Rankings 2010-2022) and is No.2 in the UK for research power (Research Excellence Framework 2021).

www.ucl.ac.uk

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Reposted by Cenk Celik

Maria Secrier @mariasecrier.bsky.social · 22d

Come do some cool cell cycle science with the awesome @alexisbarr.bsky.social and me! 🔬✨

We’re looking for an enthusiastic computational biologist / data scientist (4-year postdoc) to dive into loads of cancer genomics & transcriptomics data.

Details below. Please share!

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Reposted by Cenk Celik

Alexis Barr @alexisbarr.bsky.social · 22d

@mariasecrier.bsky.social & I are looking for an enthusiastic & excellent data scientist for a 4-year postdoc to understand cell cycle dysregulation in cancer.

Deadline 15th October. Get in touch if you have any questions.

Please repost!

More details:
www.imperial.ac.uk/jobs/search-...

Description

Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

www.imperial.ac.uk

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Reposted by Cenk Celik

Alexis Barr @alexisbarr.bsky.social · Sep 3

Feeling very fortunate to be awarded a Programme Foundation Award from CRUK @cruk-si.bsky.social

This is a new area for the lab & lets us team up with @mariasecrier.bsky.social to tackle a big problem of how different cancers lose control of proliferation

MRC Laboratory of Medical Sciences @mrc-lms.bsky.social · Sep 3

Congratulations to @alexisbarr.bsky.social and Jesus Gil who have received funding awards, together totalling around £3M, from @cancerresearchuk.org!

They will lead two exciting projects that could result in discoveries that make a real difference to the lives of people with cancer in the future.

LMS scientists receive funding to boost cancer research

Cancer Research UK has awarded significant funding to researchers at the MRC Laboratory of Medical Sciences (LMS) to lead two exciting new projects that could result in discoveries that make a real di...

lms.mrc.ac.uk

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Reposted by Cenk Celik

Bilimler Köyü @bilimler.bsky.social · Aug 14

Bu hafta “Yapay Zekanın Politik Ekonomisi” etkinliğinde Altuğ Yalçıntaş hocamız “büyük veri” meselesini iktisadi ve siyasal boyutlarıyla ele alırken, aynı saatlerde Cenk Çelik hocamız Tek Hücre ve Uzamsal Boyutta Canlılık” atölyesinde “hücreler arası iletişim konusunu masaya yatırıyordu.

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Reposted by Cenk Celik

Maria Secrier @mariasecrier.bsky.social · Aug 12

We recently published a review reflecting on challenges and opportunities in characterising cancer cell states and niches using spatial transcriptomics and integration with digital pathology, see full thread below. Thank you Molecular Oncology for the opportunity!

Cenk Celik @cenkcelik.bsky.social · Jul 26

We, Secrier Lab UCL @ugiatucl.bsky.social Genetics Institute, discussed challenges in cell state identification using spatial transcriptomics in cancer research, now out in Molecular Oncology.
 doi.org/10.1002/1878... #SpatialTranscriptomics #CancerResearch #SpatialNiches

doi.org

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Reposted by Cenk Celik

Guillaume Thibault @gthibault.bsky.social · Aug 11

📢 Our new preprint is out! We show how the common gut bacterium 𝘌. 𝘧𝘢𝘦𝘤𝘢𝘭𝘪𝘴 stops wound healing. It uses a metabolic pathway, extracellular electron transport (EET), to stress host cells, halting their migration. Watch WT bacteria (orange) stop the cells while the mutant (blue) doesn't!

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Reposted by Cenk Celik

Bilimler Köyü @bilimler.bsky.social · Aug 4

Bilimler Köyü'nde gelecek hafta...
📍 Detaylı bilgi ve başvuru: bilimler.org/etkinlikler/

#bilimlerköyü
#villageofsciences

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Cenk Celik @cenkcelik.bsky.social · Jul 26

Read the full review here: doi.org/10.1002/1878.... Exciting times for spatial cancer biology.  Thanks to @mariasecrier.bsky.social and all co-authors!
#SpatialOmics #AI #Cancer

doi.org

Cenk Celik @cenkcelik.bsky.social · Jul 26

ST can uncover biomarkers of therapy response, resistance niches and new targets. We discuss how integration with pathology and AI can bridge the gap to patient care.

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Cenk Celik @cenkcelik.bsky.social · Jul 26

Linking ST with histology and AI could make spatial insights accessible in the clinic. We outline current approaches, from gene expression prediction to super-resolution mapping.

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Cenk Celik @cenkcelik.bsky.social · Jul 26

Graph neural networks, geospatial statistics and self-supervised learning are transforming niche detection and cell–cell communication analysis.

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Cenk Celik @cenkcelik.bsky.social · Jul 26

Niches are ecosystems of interacting cells driving immune evasion and therapy resistance. We review statistical, geospatial and AI-based tools to detect and model these niches.

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Cenk Celik @cenkcelik.bsky.social · Jul 26

Cell identity is more than type. States like EMT or T-cell exhaustion shape tumour behaviour. We discuss methods to capture these states and why spatial context changes the game.

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Cenk Celik @cenkcelik.bsky.social · Jul 26

Key challenges in ST for cancer 
(a) Defining cell states beyond cell types
 (b) Characterising cellular niches and interactions 
(c) Integrating spatial data with other modalities for clinical use

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Cenk Celik @cenkcelik.bsky.social · Jul 26

Spatial transcriptomics (ST) is changing how we study cancer. It maps gene expression to tissue structure, revealing how cells interact within the tumour microenvironment. But big challenges remain. Here’s what we cover.

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Cenk Celik @cenkcelik.bsky.social · Jul 26

We, Secrier Lab UCL @ugiatucl.bsky.social Genetics Institute, discussed challenges in cell state identification using spatial transcriptomics in cancer research, now out in Molecular Oncology.
 doi.org/10.1002/1878... #SpatialTranscriptomics #CancerResearch #SpatialNiches

doi.org

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Reposted by Cenk Celik

UCL Genetics Institute @ugiatucl.bsky.social · Jun 3

New preprint from the Secrier lab. @cenkcelik.bsky.social @mariasecrier.bsky.social present EnrichMap, a Python package to compute gene set enrichment scores in spatial transcriptomics data: tinyurl.com/yc48f4fx.

See an explainer thread from @cenkcelik.bsky.social here: bsky.app/profile/cenk....

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Reposted by Cenk Celik

Maria Secrier @mariasecrier.bsky.social · Jun 2

Want to uncover biologically meaningful patterns in spatial omics data? Check out our new method EnrichMap, details below. Work led by the brilliant @cenkcelik.bsky.social! #spatialomics #genesets

Cenk Celik @cenkcelik.bsky.social · Jun 2

[Preprint alert]
We’re thrilled to introduce EnrichMap: a powerful new method for spatial gene set enrichment. It’s spatially aware, biologically meaningful and built for the next generation of spatial transcriptomics. www.biorxiv.org/content/10.1...

Description of a computational method for computing biological signals in spatial transcriptomics.

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Cenk Celik @cenkcelik.bsky.social · Jun 2

Thanks all members of @mariasecrier.bsky.social lab for their comments and critique during the development of EnrichMap.

Cenk Celik @cenkcelik.bsky.social · Jun 2

Want a sneak peek or to try it on your own data? Try EnrichMap enrichmap.readthedocs.io/en/latest/
#SpatialTranscriptomics #ComputationalBiology #EnrichMap #spatialomics

Welcome to EnrichMap’s documentation! — EnrichMap

enrichmap.readthedocs.io

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Cenk Celik @cenkcelik.bsky.social · Jun 2

Generalisable to any tissue.
EnrichMap isn’t just for tumours – it’s for anyone working with spatial transcriptomics.

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Cenk Celik @cenkcelik.bsky.social · Jun 2

We’ve designed it to be fast, flexible and easy to use:
- Works seamlessly with Scanpy, Squidpy and AnnData (@scverse_team compatible)
- Plug-and-play any ST dataset
- Outputs spatially informed scores
- Geostatistics-inspired metrics to evaluate gene sets

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Cenk Celik @cenkcelik.bsky.social · Jun 2

What can EnrichMap do?
- Correct for spatial confounders
- Support batch correction and gene weighting
- Map gradients of tumour and immune programmes
- Compare microenvironments
- Reveal niche-specific signalling

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Cenk Celik @cenkcelik.bsky.social · Jun 2

Why does this matter?
Tumours are messy. Immune niches are local. Cell states vary in space. If you’re collapsing expression without space, you’re missing the story. EnrichMap keeps that story intact.

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