Contact us by email if you meet the eligibility criteria and are interested in applying based on our project outline. Your email should include your project proposal, a CV and two reference letters. We look forward to hearing from you.

Project Outline Nr. 58: drive.google.com/file/d/1YZbs...

Important information:
- A minimum of one first-author publication is required
- Applicants must develop their own research proposal based on our project outline
- Provide your CV, two reference letters and your project proposal
- Expected start date: between August 1, 2026, and January 1, 2027

SCP enables the quantification of thousands of proteins per individual cell, thereby revealing cell states, regulatory mechanisms, and functional heterogeneity. Join us in developing a framework to analyze comprehensive SCP datasets (up to 6000 quantified proteins per cell!).

Many thanks to all authors: @dbdimitrov.bsky.social, Stefan Schrod, @mrohbeck.bsky.social, and @oliverstegle.bsky.social.
@embl.org | @dkfz.bsky.social | @uniheidelberg.bsky.social | @sangerinstitute.bsky.social

We further describe how these methods achieve the 3 key aims of causal modelling:
1️⃣ Understand perturbation responses
2️⃣ Extrapolate to unseen conditions
3️⃣ Guide future experiments

We map how these methods commonly utilise partial views of causal signatures (perturbations ⚡, temporal ⏳, spatial 📍& multi-omics 🧬) and rely on a shared core modelling concepts (from Disentanglement to Mechanistic Discovery).

Explore the tools covered in our review in an online repository: interp-extrap-perturb.readthedocs.io 💻
This database is continuously growing, and we invite everyone to submit methods and help us keep the repository up-to-date.

We review and connect >150 methods to help you choose the most suitable method for a given biological task and dataset.
Our perspective further proposes a unifying ontology to structure and organise these methods across tasks, assumptions, and modelling concepts.

Many thanks to @michaelboutros.bsky.social, all our collaborators at @embl.org and @dkfz.bsky.social, and our funders!

📘Preprint: www.biorxiv.org/content/10.6... 10/10

scPT-seq directly links genotype, expression, lineage & space in vivo. A powerful framework for functional genomics beyond indirect CRISPR readouts. 9/10

CRISPR edits also act as heritable clonal markers.
We reconstruct lineages, transfer spatial information between cells, and uncover region-specific stem cell identities and perturbation responses. 8/10

scPT-seq also enables dosage-dependent analysis:
Different cell types respond differently to mono- vs biallelic mutations, revealing spatially organized compensatory mechanisms across the tissue. 7/10

Key insight:
Standard perturbed-vs-control comparisons are dominated by stress responses.
Using true internal WT cells, scPT-seq uncovers mutation-specific transcriptional programs that were previously hidden. 6/10

We applied scPT-seq to the Drosophila midgut, a regenerative tissue with strong spatial structure.
This lets us compare mutant and wild-type cells within the same tissue, separating genetic from environmental effects. 5/10

What do we gain?
1️⃣ Base-pair resolution of CRISPR edits
2️⃣ Detection of insertions, deletions and splice changes
3️⃣ Clear distinction between WT, mono- and biallelic edits
4️⃣ Identification of “missing” alleles (a major blind spot of past methods) 4/10

scPT-seq combines:
• droplet-based scRNA-seq
• targeted long-read sequencing of edited loci
• haplotype-resolved mutation calling
All from the same cells, in vivo. 3/10

The problem:
Guide capture ≠ successful edit.
Computational inference ≠ true genotype.
And in vivo, environmental effects easily mask real mutation-driven responses.
So how do we truly link genotype to phenotype at single-cell resolution? 2/10

You’ll help build interoperable, FAIR tools across @scverse.bsky.social and @bioconductor.bsky.social ecosystems. You will work together with a cross-institute team composed of @lucamarconato.bsky.social, @arturmansl.bsky.social and many contributors from #scverse and #Bioconductor!