Peter Krenn

spaXio - MSCA doctoral network - News News

We are still seeking the right candidates for Projects 12 and 13, and have therefore reopened the application process. We are looking for two motivated bioinformaticians eager to help unravel metastatic processes in colon and breast cancer.

Details: www.spaXio.eu/news
Deadline: 18 February 2026

Open positions for 11 scientists! 

Our newly funded consortium "EpiFlaMe" is looking for 7 PhD students, 2 bioinformaticians (postdoc and technician), and 2 wet lab technicians.

Interested? Submit your application until Feb 13, 2026 via www.plus.ac.at/epiflame

🚀 Prophet v3 is out!
AI that predicts how cells respond to genetic & chemical perturbations across readouts.
Now scales to 1.9 M molecules + in vitro validation of melanoma-specific hits 🧬💊
📄 biorxiv.org/content/10.1...
#AI #Biology #DeepLearning

Less than a week left to apply!

Join the spaXio Doctoral Network, where we’re decoding the biology of metastasis through spatial omics, organoid models, and computational biology.
Don’t miss your chance to be part of this cutting-edge research community.
Apply now: www.spaXio.eu

Better understanding of laboratory animal genetics will improve reproducibility Incomplete characterization and inconsistent reporting of laboratory animal genetics undermine study quality and limit research reproducibility. This Perspective highlights the LAG-R guidelines and…

Incomplete characterization and inconsistent reporting of laboratory animal #genetics undermine study quality and limit research #reproducibility. @reproducibilityexp.bsky.social highlight the LAG-R guidelines and call for collective action to enhance scientific integrity.🧪

Pre-print alert! And this one really is a must read for anyone that does spectral #flowcytometry. It is a complete, fully-automated spectral unmixing pipeline that reduces error up to 9000-fold.

Want to get a tough sample, like lung, looking like this? Read more!

www.biorxiv.org/content/10.1...

Join spaXio, an EU-funded MSCA Doctoral Network exploring how cancer spreads & interacts with its surroundings using spatial multi-omics, 3D tumoroids, advanced imaging & AI.

🎓 14 fully funded PhD positions across Europe!
🌐 www.spaXio.eu
📝 Apply: civis.smapply.io/prog/spaxio_...

SLAM passes the haematopoietic stem cell identity test Nature Reviews Molecular Cell Biology, Published online: 02 October 2025; doi:10.1038/s41580-025-00906-4Christina Termini highlights the importance of the identification of haematopoietic stem cell markers.

ICYMI: New Online! SLAM passes the haematopoietic stem cell identity test

A platform of robust patient-derived leukemia models covering subgroups for which no cell lines exist Preclinical cancer research requires robust model systems, especially for poor prognosis entities like acute myeloid leukemia (AML), a highly aggressive blood cancer. Here, primary tumor cells from 13...

🚨 New preprint alert! 🚨

We just posted our latest manuscript on patient-derived xenograft (PDX) models in acute myeloid leukemia (AML):

📝 "A platform of robust patient-derived leukemia models covering subgroups for which no cell lines exist"

www.biorxiv.org/content/10.1...

Why this matters ⬇️

Happy to share that my PhD has finally taken the shape of a paper! ✨

Huge thanks to all authors, especially @davidbrueckner.bsky.social & @ehannezo.bsky.social for leading the modeling and @raimonsunyer.bsky.social & @xaviertrepat.bsky.social for their invaluable supervision.

🧵👇

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...

The integrin odyssey – a journey full of fundamental discoveries Summary: This Perspective highlights the key discoveries in integrin research that laid the foundation for a successful field.

“The integrin odyssey – a journey full of fundamental discoveries” by Fässler and Sonnenberg in @jcellsci.bsky.social, worth a read!
journals.biologists.com/jcs/article/...

Epithelial tension controls intestinal cell extrusion Cell extrusion is essential for homeostatic self-renewal of the intestinal epithelium. Extrusion is thought to be triggered by crowding-induced compression of cells at the intestinal villus tip. In th...

1/11 In @science.org: A new perspective on how our intestines renew. Cells are not “pushed out” by crowding or die from apoptosis. Instead, cells play a mechanical tug-of-war, where weaker cells extrude, reframing gut renewal as force-regulated. www.science.org/doi/10.1126/...

Spatial joint profiling of DNA methylome and transcriptome in tissues - Nature DNA-methylation and gene-expression profiling of tissue sections at near single-cell resolution can be used to create detailed spatial maps showing how methylation and transcription interact to shape ...

What a step forward for spatial biology! Combining RNA profiling with DNA methylation detection while maintaining tissue context is pure awesomeness! A must read 🔍 www.nature.com/articles/s41...

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.

www.nature.com/articles/s41...

spaXio members were proud to take part in the Summer School "Immuno-Oncology in the Spatial Omics Era", hosted by the Institut Cancer et Immunologie (ICI) Marseille and CIVIS. It was a fantastic week filled with cutting-edge scientific talks, hands-on workshops, and inspiring student presentations.

Dynamic regulation of integrin β1 phosphorylation supports invasion of breast cancer cells - Nature Cell Biology Conway et al. show that integrin β1 phosphorylation is regulated through balanced activities of tyrosine kinases, such as Src and Arg, and phosphatases, such as PTP-PEST and Shp2, facilitating invadop...

Latest from @ivaskalab.bsky.social @jrwconway.bsky.social in NCB. We find that SHP-2 inhibition stops TNBC invasion and limits metastasis by blocking integrin dephosphorylation!

Read more at:

www.nature.com/articles/s41...

Big news from Uni Salzburg! The Xenium spatial transcriptomics platform is up and running. Supported by FFG-backed CellComm initiative, Centre for Tumour Biology and Immunology and Dept of Biosciences and Med.Biology, this tech brings next-level spatial resolution to our cancer research efforts!

What a day! First our granted MSCA doctoral network spaXio @spaxio.bsky.social, now my first last authorship! Perfect timing as we will need to do some serious organoid manipulations to achieve our spaXio goals!

Check out our protocol: pubmed.ncbi.nlm.nih.gov/40163310

Thrilled to announce our doctoral network for spatial oncology as been funded by Marie Skłodowska-Curie Actions! This combines some of the best immuno-oncology and computational labs across Europe to create a multi-disciplinary PhD program for spatial-omics cancer research. More details soon!

Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution - Nature Communications Deciphering the features, structure, and functions of the cell niche in tissues remains a major challenge. Here, the authors develop scNiche, a computational framework to identify and characterise cel...

Exciting computational workflow and a step towards understanding the ACTUAL composition of celltype specific niches. www.nature.com/articles/s41...