Stegle Lab
@steglelab.bsky.social
Our group develops and applies computational approaches to study molecular variations and their phenotypic consequence. We are part of DKFZ and EMBL.
Website: https://steglelab.org/
Website: https://steglelab.org/
Pinned
Stegle Lab
@steglelab.bsky.social
· Dec 9
We are the Stegle Lab: A bioinformatics group advancing computational methods to study molecular variations and their impact on phenotypes. We are jointly hosted at the German Cancer Research Center (@dkfz.bsky.social) and the European Molecular Biology Laboratory (@embl.org) in Heidelberg, Germany.
Reposted by Stegle Lab
📢 3rd Keynote reveal!
We’re excited to welcome Prof. Dr. Oliver Stegle as keynote speaker at #HMCConference2026
Director & Co-Spokesperson of #GHGA, @oliverstegle.bsky.social advances secure, #FAIR infrastructures for data-driven biomedical research. 🧬
steglelab.bsky.social ghga.bsky.social
We’re excited to welcome Prof. Dr. Oliver Stegle as keynote speaker at #HMCConference2026
Director & Co-Spokesperson of #GHGA, @oliverstegle.bsky.social advances secure, #FAIR infrastructures for data-driven biomedical research. 🧬
steglelab.bsky.social ghga.bsky.social
February 10, 2026 at 11:46 AM
📢 3rd Keynote reveal!
We’re excited to welcome Prof. Dr. Oliver Stegle as keynote speaker at #HMCConference2026
Director & Co-Spokesperson of #GHGA, @oliverstegle.bsky.social advances secure, #FAIR infrastructures for data-driven biomedical research. 🧬
steglelab.bsky.social ghga.bsky.social
We’re excited to welcome Prof. Dr. Oliver Stegle as keynote speaker at #HMCConference2026
Director & Co-Spokesperson of #GHGA, @oliverstegle.bsky.social advances secure, #FAIR infrastructures for data-driven biomedical research. 🧬
steglelab.bsky.social ghga.bsky.social
Working on trans-eQTL mapping with population-scale scRNA-seq? Meet LIVI, our latest framework that enables efficient trans-eQTL mapping at single-cell resolution across cohorts of hundreds to thousands of donors.
Preprint: doi.org/10.64898/202...
Summary in the 🧵 below by @danaivagiaki.bsky.social
Preprint: doi.org/10.64898/202...
Summary in the 🧵 below by @danaivagiaki.bsky.social
February 10, 2026 at 8:59 AM
Working on trans-eQTL mapping with population-scale scRNA-seq? Meet LIVI, our latest framework that enables efficient trans-eQTL mapping at single-cell resolution across cohorts of hundreds to thousands of donors.
Preprint: doi.org/10.64898/202...
Summary in the 🧵 below by @danaivagiaki.bsky.social
Preprint: doi.org/10.64898/202...
Summary in the 🧵 below by @danaivagiaki.bsky.social
We are hiring a Research Software Engineer at @embl.org Heidelberg to enhance and maintain open-source infrastructure for spatial omics.
🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
Research Software Engineer - Spatial-omics
The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...
embl.wd103.myworkdayjobs.com
February 2, 2026 at 2:54 PM
We are hiring a Research Software Engineer at @embl.org Heidelberg to enhance and maintain open-source infrastructure for spatial omics.
🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
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...
Project Outline Nr. 58: drive.google.com/file/d/1YZbs...
Alliance_project-outline Stegle Krijgsveld.pdf
drive.google.com
January 20, 2026 at 9:43 AM
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...
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
- 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
January 20, 2026 at 9:43 AM
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
- 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!).
January 20, 2026 at 9:43 AM
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!).
Together with Jeroen Krijgsveld, we are looking for a postdoc to help us unlock single-cell proteomics (SCP) through the establishment of a scalable computational framework.
For more information, see the @hlsalliance.bsky.social Postdoc Program:
www.health-life-sciences.de/opportunitie...
For more information, see the @hlsalliance.bsky.social Postdoc Program:
www.health-life-sciences.de/opportunitie...
HEALTH + LIFE SCIENCE ALLIANCE | Interinstitutional Postdocs
www.health-life-sciences.de
January 20, 2026 at 9:43 AM
Together with Jeroen Krijgsveld, we are looking for a postdoc to help us unlock single-cell proteomics (SCP) through the establishment of a scalable computational framework.
For more information, see the @hlsalliance.bsky.social Postdoc Program:
www.health-life-sciences.de/opportunitie...
For more information, see the @hlsalliance.bsky.social Postdoc Program:
www.health-life-sciences.de/opportunitie...
We're organizing a one-day, in-person workshop on trustworthy healthcare AI, with leading experts discussing key dimensions such as robustness, fairness, privacy, explainability, and clinical validation.
Register now and submit your poster: elsa-ai.eu/elsa-worksho...
📅 March 9, Heidelberg DE
Register now and submit your poster: elsa-ai.eu/elsa-worksho...
📅 March 9, Heidelberg DE
January 15, 2026 at 10:09 AM
We're organizing a one-day, in-person workshop on trustworthy healthcare AI, with leading experts discussing key dimensions such as robustness, fairness, privacy, explainability, and clinical validation.
Register now and submit your poster: elsa-ai.eu/elsa-worksho...
📅 March 9, Heidelberg DE
Register now and submit your poster: elsa-ai.eu/elsa-worksho...
📅 March 9, Heidelberg DE
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
@embl.org | @dkfz.bsky.social | @uniheidelberg.bsky.social | @sangerinstitute.bsky.social
January 7, 2026 at 9:53 AM
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
@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
1️⃣ Understand perturbation responses
2️⃣ Extrapolate to unseen conditions
3️⃣ Guide future experiments
January 7, 2026 at 9:53 AM
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
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).
January 7, 2026 at 9:53 AM
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.
This database is continuously growing, and we invite everyone to submit methods and help us keep the repository up-to-date.
Interpretation, Extrapolation, and Perturbation of Single Cells — Interpretation, Extrapolation, and Perturbation of Single cells
interp-extrap-perturb.readthedocs.io
January 7, 2026 at 9:53 AM
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.
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.
Our perspective further proposes a unifying ontology to structure and organise these methods across tasks, assumptions, and modelling concepts.
January 7, 2026 at 9:53 AM
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.
Our perspective further proposes a unifying ontology to structure and organise these methods across tasks, assumptions, and modelling concepts.
Fresh off the press in 2026! Interested in the challenge of how to advance from descriptive atlases to causal mechanisms and counterfactuals? 🔬
Take a look at our recent perspective: "Interpretation, extrapolation and perturbation of single cells"! (rdcu.be/eXeDY)
Take a look at our recent perspective: "Interpretation, extrapolation and perturbation of single cells"! (rdcu.be/eXeDY)
Interpretation, extrapolation and perturbation of single cells
Nature Reviews Genetics - Causal and mechanistic modelling strategies, which aim to infer cause–effect relationships, provide insights into cellular responses to perturbations. The authors...
rdcu.be
January 7, 2026 at 9:53 AM
Fresh off the press in 2026! Interested in the challenge of how to advance from descriptive atlases to causal mechanisms and counterfactuals? 🔬
Take a look at our recent perspective: "Interpretation, extrapolation and perturbation of single cells"! (rdcu.be/eXeDY)
Take a look at our recent perspective: "Interpretation, extrapolation and perturbation of single cells"! (rdcu.be/eXeDY)
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
📘Preprint: www.biorxiv.org/content/10.6... 10/10
Direct detection of CRISPR mutations and transcriptional responses at single cell resolution in vivo
CRISPR screens coupled with single-cell RNA sequencing are transforming high-throughput functional genomics. However, applications in vivo remain limited and are confounded by difficulties in identify...
www.biorxiv.org
December 27, 2025 at 4:13 PM
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
📘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
December 27, 2025 at 4:13 PM
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
We reconstruct lineages, transfer spatial information between cells, and uncover region-specific stem cell identities and perturbation responses. 8/10
December 27, 2025 at 4:13 PM
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
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
Different cell types respond differently to mono- vs biallelic mutations, revealing spatially organized compensatory mechanisms across the tissue. 7/10
December 27, 2025 at 4:13 PM
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
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
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
December 27, 2025 at 4:13 PM
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
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
This lets us compare mutant and wild-type cells within the same tissue, separating genetic from environmental effects. 5/10
December 27, 2025 at 4:13 PM
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
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
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
December 27, 2025 at 4:13 PM
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
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
• droplet-based scRNA-seq
• targeted long-read sequencing of edited loci
• haplotype-resolved mutation calling
All from the same cells, in vivo. 3/10
December 27, 2025 at 4:13 PM
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
• 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
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
December 27, 2025 at 4:13 PM
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
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
How do CRISPR edits actually change cells in real tissues?
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
December 27, 2025 at 4:13 PM
How do CRISPR edits actually change cells in real tissues?
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10
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!
December 27, 2025 at 3:50 PM
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!