Nik Fortelny

Applications are open for to our Doctoral Network on spatial biology and immuno-oncology! Our project is #14.

Deadline: November 8th, 2025

Postdoc position open!
Digital Pathology: Therapy-response prediction using spatial biology
University of Salzburg
Deadline: October 26th, 2025

We look forward to hearing from you!

www.plus.ac.at/biowissensch...

Differences between in vivo and ex vivo hematopoietic model systems modulate the outcomes of genetic perturbations. Ex vivo cell cultures are reductionist models that enable cost effective, precisely controlled experiments with fewer ethical concerns than in vivo conditions. This results in their extensive use in d...

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

Our results highlight molecular differences between model systems that can be used to improve ex vivo models - and they provide an interesting test case for perturbation prediction tools.

Most strikingly, cells ex vivo have lower interferon signatures and this translates to differences in KO effects ex vivo versus in vivo, especially when perturbing regulators involved in interferon responses. These differences were not predicted using current perturbation prediction tools.

What are the differences between cells ex vivo and in vivo and how does this affect responses to experimental perturbations?

Aarathy from our group compared the transcriptome of hematopoietic cells cultured ex vivo to those grown in vivo using two KO datasets (Perturb-seq and genetic KOs).

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Thank you #MUV for awarding @nikfortelny.bsky.social and me with the Researcher of the Month award for our recent publication in @natureportfolio.nature.com Nature Immunology. Very proud and we will continue with excellent science tailored to identifying novel therapies for precision medicine.

In combination with existing local expertise in tumor biology and immunology and existing technologies from spatial omics to computational biology, these professorships will strengthen our ability to systematically dissect health and disease.

Application deadline: April 19th, 2025

ANIMAL PHYSIOLOGY focused on studying biological (e.g. oncological, immunological, infection-biological, neurophysiological and age-associated) processes in health and disease by developing and establishing relevant model systems.
tinyurl.com/AnimalPhysio...

MEDICAL SYSTEMS BIOLOGY focused on modern/innovative methods to generate new systems biology data to characterise complex biological systems with high throughput (e.g. functional /CRISPR screens, single cell sequencing, spatial and temporal biology, and/or drug screens).
tinyurl.com/MedSysBioSal...

We are hiring two tenured full-time professors in Salzburg, Austria!

Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics
go.bsky.app/73rcuJn

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8

“But the eggs were just so expensive.”

Please add me thanks!

Baseline JAK–STAT signaling maintains immune cell homeostasis Nature Immunology - Homeostatic immune cells remain perpetually vigilant against pathogens. We found that baseline JAK–STAT signaling supports the characteristic transcriptional and...

Thanks Nature Immunology for highlighting our paper with a Research Briefing, explaining the broader relevance with a bit of backstory and quotes from a reviewer and the editor. The paper is open access, but the Research Briefing is not – please use the following link for free access: rdcu.be/dGnH0

Started during my postdoc but has now come to fruition!

Systematic analyses of JAK-STAT signaling show the intriguing roles of this classical immune-response pathway in homeostasis.

A big thanks to a whole consortium of experimental collaborators for a massive dataset!