Cenk Celik

Enterococcus faecalis-derived lactic acid suppresses macrophage activation to facilitate persistent and polymicrobial wound infections Macrophage activation is essential for innate immunity and antimicrobial defense. We show that Enterococcus faecalis suppresses macrophage activation …

Lactic acid lover? Check out @ronni.bsky.social 's new work in
@cp-cellhostmicrobe.bsky.social showing how Enterococcus faecalis-derived LA suppresses macrophage activation, in turn promoting bacterial persistence and polymicrobial wound infection in vivo.
www.sciencedirect.com/science/arti...

We are also recruiting a Postdoc in cell/molecular biology!

3yr, fully funded by @cancerresearchuk.org more details here: news.cancerresearchuk.org/2025/11/27/s...

Apply here: www.imperial.ac.uk/jobs/search-...

Reimagining Health with Big Data | Norwich Science Festival Dr Marina Escalera Zamudio and Dr Cenk Celik will share the ways in which big data and AI are transforming medicine.

See UGI's Dr Marina Escalera Zamudio (Rosetrees Fellow) and Dr Cenk Celik (Research Fellow) @cenkcelik.bsky.social presenting at the Norwich Science Festival @niscifest.bsky.social session on "Reimagining Health with Big Data".

norwichsciencefestival.co.uk/whats-on/rei...

#NISF26

Proud of this international effort led by NTU Singapore, @scelse.bsky.social and the University of Geneva.

Huge props to first author @aarontan.bsky.social and my co-lead @kimingeneva.bsky.social and other authors including @cenkcelik.bsky.social.

#ScienceAdvances #Microbiology #NTUsg

Have you ever heard that women have more chances than men of getting grants or positions in academia? Of course you have, and here are my personal views on this. With the shocking revelation that no, it is NOT TRUE ! (1/n)

There's still a few days left to apply for our AI-Intervene PhD project mapping the drivers of avian influenza using viral genomics, bird migration data and AI-powered phylodynamics.

Come join us! Details below.

#FindaPhD #LondonPhD #genomics

Great talk from @ugiatucl.bsky.social post-doc @cenkcelik.bsky.social presenting his work developing new approaches to explore the spatial patterns of cancer evolution.

Preprint 👉 www.biorxiv.org/content/10.1...

Thanks for giving our last seminar of the year!

We’re live!
iMeanIt – Highlight Words. Forever.
✨ Highlight. Note. Remember. All while browsing.
1️⃣ Highlight anything on a webpage. Your highlights stay—refresh or revisit, they’re still there.
2️⃣ Add notes instantly. Tap a word → view or edit annotations in seconds.

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).

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

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!

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...

@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-...

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

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.

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!

📢 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!

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

#bilimlerköyü
#villageofsciences

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

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.

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.

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

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.

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.

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

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.

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

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....

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

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

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

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