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Stegle Lab

@steglelab.bsky.social
791 followers 145 following 125 posts

Our group develops and applies computational approaches to study molecular variations and their phenotypic consequence. We are part of DKFZ and EMBL. Website: steglelab.org

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Stegle Lab @steglelab.bsky.social · 07/10/2026
Excited to share that our lab will be at #NeurIPS2026 with 2 papers! 🎉 Our first NeurIPS submissions since 2015, and both got in on the first try: one on temporal point processes, one on counterfactual queries on tissue graphs. Paper threads coming soon. See you in Paris & Sydney! 👋
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Brian Clarke @brianfclarke.bsky.social · 17/08/2026
1/4 Job alert: Our group is looking for a postdoc for a three-year position in an international collaboration with Marc Jan Bonder and @science-wallet.bsky.social. Recruiting is through the DKFZ International Postdoc Program: www.dkfz.de/en/karriere/... Deadline: September 8
dkfz.de
DKFZ Postdoctoral Fellowships - German Cancer Research Center
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Stegle Lab @steglelab.bsky.social · 11/08/2026
📅 Register by August 16th: event.sdu.dk/mopitas2026/... Looking forward to welcoming you to Copenhagen, together with Richard Röttger, Jakub Sedzinski, @itisalist.bsky.social, @oliverstegle.bsky.social and all the rest of the MOPITAS team.
event.sdu.dk
MOPITAS Autumn School 2026
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Stegle Lab @steglelab.bsky.social · 11/08/2026
Our lab will focus on data representation and segmentation, and cell-cell communication - with our developers Elyas Heidari and @dbdimitrov.bsky.social walking you through their latest methods and approaches.
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Stegle Lab @steglelab.bsky.social · 11/08/2026
The school runs in a dynamic, hands-on format: ▫️Mornings will be dedicated to insightful talks and lectures ▫️Afternoons will focus on collaborative mini-projects, allowing participants to apply what they’ve learned in a practical setting.
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Stegle Lab @steglelab.bsky.social · 11/08/2026
📢 Deadline extended! The application deadline for our MOPITAS Autumn School on Spatial Transcriptomics Data Analysis, taking place October 12-14th in Copenhagen, has been pushed to August 16th. This is a great chance to sharpen your expertise in data science and multi-omics analysis. Register now!
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Stegle Lab @steglelab.bsky.social · 06/08/2026
Did you know that our group at @embl.org is helping to decode the health of tropical forests? Think of it as spatial omics at a whole new scale: satellite imagery meets the DNA and RNA of soil microbes revealing hidden biological patterns in complex ecosystems.
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Stegle Lab @steglelab.bsky.social · 05/08/2026
Two weeks left to apply! We're recruiting a PhD student with @brianfclarke.bsky.social and @junyanlu.bsky.social through HIDSS4Health - see below for details. 👇 Looking forward to your application.
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Stegle Lab @steglelab.bsky.social · 05/08/2026
Happy to welcome Mădălina to the lab! As a postdoc at @embl.org, she will develop computational methods for spatial omics to investigate how cellular organization and tumor heterogeneity contribute to cancer progression and disease relapse.
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Stegle Lab @steglelab.bsky.social · 06/07/2026
Welcome to our team, Tomaz Vieira! He will be working on “SpatialData”, a software framework for processing spatial omics data, and more in general in the data format standardization efforts of the @scverse-team.bsky.social consortium, a research software infrastructure for single-cell biology.
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EMBL @embl.org · 29/06/2026
What happens when AI and biology accelerate each other? EMBL Acting Head of AI Centre, Oliver Stegle, discusses how closer integration of these fields could transform the life sciences. Watch this video to learn more. #EMBL_AI
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Helmholtz Metadata Collaboration @helmholtzhmc.bsky.social · 30/04/2026
Day 3 of #HMCConference2026 opened with a keynote by Prof Dr Oliver Stegle on how metadata powers large-scale genomic research. The talk showed how interoperable metadata enables data integration, reproducibility, and analysis at scale – making it a core foundation of research infrastructures.
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Stegle Lab @steglelab.bsky.social · 23/04/2026
Grateful to editor @linkonrg.bsky.social and artist Patrick Morgan for translating these concepts into a compelling visual narrative, to all collaborators and those who have contributed to our living catalogue of single cell perturbation methods: interp-extrap-perturb.readthedocs.io/en/latest/me...
interp-extrap-perturb.readthedocs.io
All Methods — Interpretation, Extrapolation, and Perturbation of Single cells
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Stegle Lab @steglelab.bsky.social · 23/04/2026
The cell is the ball, the bumpers are causal signatures shaping its path, and the flippers are the emerging methods that guide our understanding as it moves through the complex molecular terrain. Link to our review: doi.org/10.1038/s415...
doi.org
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 review computational approaches that ...
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Stegle Lab @steglelab.bsky.social · 23/04/2026
Are you ready to play our special version of pinball? 🕹️ This cover of @natrevgenet.nature.com was inspired by our review on the interpretation, extrapolation and perturbation of single cells. The artwork takes the form of a pinball machine, as a deliberate reimagination of Waddington's metaphor.
An illustration of a pinball machine representing a cell as the ball, with bumpers as causal signatures and flippers as methods guiding understanding through complex molecular terrain.
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Karsten Rippe @karsten-rippe.bsky.social · 20/04/2026
5/ Ezgi Sen, a great PhD student in the Rippe and Stegle labs, led the downstream analysis: Atera clearly resolved 15 main cell clusters on one CRC section. Non-malignant epithelium splits into absorptive and secretory lineages with LGR5+ stem cells at the crypt bases.
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Stegle Lab @steglelab.bsky.social · 01/04/2026
Two weeks ago, MAIGE group leader @brianfclarke.bsky.social and Katharina, together with Dominik (Steinmetz lab) joined #Perturb2026, exploring new technologies and datasets. Highlight: Katharina’s first short talk on large-scale perturbation screens in cardioids and great discussions at our poster!
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Stegle Lab @steglelab.bsky.social · 31/03/2026
Join us for a postdoc in AI in human genetics at @embl.org in close collaboration with Adrian Cortes (GSK) and @brianfclarke.bsky.social - exploring the effects of rare variants using population-scale cohorts and single-cell readouts. 🔗 Apply now: embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
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Deutsches Krebsforschungszentrum (DKFZ) @dkfz.bsky.social · 18/03/2026
Do you want to do your #postdoc in #cancerresearch with the most prestigious fellowship in Europe? Apply to DKFZ #MSCA MasterClasses by May 18. 26 Projects in cancer research including #cellandmolecularbiology #genomics #bioinformatics #immunology. @horizoneu.bsky.social 👉Apply here: t1p.de/nx6tu
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Stegle Lab @steglelab.bsky.social · 18/03/2026
Welcome @bbbranjan.bsky.social! His career across single-cell genomics, 🐁 biology and software dev has been about bridging wet-lab with reliable analysis workflows. At @embl.org he will lead a collab with @vrmlnroel.bsky.social on modelling GxE interactions to dissect risk factors for human disease.
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Stegle Lab @steglelab.bsky.social · 17/03/2026
And the CAMDA Health Privacy Challenge has entered its second edition, ready for your submissions. 🚀 Get involved and find more details: benchmarks.elsa-ai.eu?ch=8&com=int...
benchmarks.elsa-ai.eu
Overview - Health (2026) - ELSA Benchmarks Platform
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Stegle Lab @steglelab.bsky.social · 17/03/2026
Thanks to CAMDA for providing the platform, and to the organizing team and all participants who helped make this effort possible. 📄 Our preprint is now available on bioRxiv - explore it here: doi.org/10.64898/202...
doi.org
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Stegle Lab @steglelab.bsky.social · 17/03/2026
We’re excited to announce the 2nd edition of the Health Privacy Challenge. 🍅🫐 What started last year as a CAMDA community challenge has grown into a benchmarking study of generative models for biologically useful and privacy-preserving synthetic omics, focusing on trade-offs across evaluation axes.👇
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Stegle Lab @steglelab.bsky.social · 12/03/2026
We are happy to have contributed to this collaborative effort combining experimental scale with computational integration. Many thanks to the whole team - especially Dewi Moonen, @anniquec.bsky.social, Lars Steinmetz, Daniel Schreivogel, Stefan Schrod, @oliverstegle.bsky.social and many others.
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Stegle Lab @steglelab.bsky.social · 12/03/2026
This work provides a genome-scale view of how noncoding variants contribute to immune disease and shows how dispersed risk loci converge on shared transcriptional programs. 📜 Preprint: www.biorxiv.org/content/10.6...
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Stegle Lab @steglelab.bsky.social · 12/03/2026
By systematically testing immune disease risk loci in the relevant cell type, we for the first time mapped the entire causal chain from variant → CRE → gene → regulatory network.
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Stegle Lab @steglelab.bsky.social · 12/03/2026
How do immune disease-relevant variants rewire gene regulation in CD4+ T cells? In a collaboration led by Daniel Schraivogel and Lars Steinmetz at @embl.org, we combined two large-scale CRISPRi screens (4.1M cells) to map the downstream cascades of thousands of SNPs.
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Stegle Lab @steglelab.bsky.social · 12/03/2026
And huge thanks to everyone who helped to make this possible. 🤝 @elsa-ai.eu @embl.org @ellisheidelberg.bsky.social
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Stegle Lab @steglelab.bsky.social · 12/03/2026
It was encouraging to see conversations emerge across disciplines, with a shared interest in advancing trustworthy AI for healthcare and continuing to build this community together 🔥 Thanks to everyone who joined, spoke, presented posters, and brought such great energy!
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Stegle Lab @steglelab.bsky.social · 12/03/2026
Discussions started from the human dimension of trust between end users and researchers, and moved toward translating uncertainty and explainability into real accountability, and how to stress-test models and develop meaningful benchmarks and metrics that strengthen trust in practice.
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Stegle Lab @steglelab.bsky.social · 12/03/2026
We wrapped up our in-person @elsa-ai.eu TrustworthyAI4Health 2026 Workshop at @embl.org on Monday. The workshop brought together experts and a community of enthusiastic researchers to explore pathways for building trust in AI for healthcare. A fuller write-up is coming soon!
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Helmholtz Metadata Collaboration @helmholtzhmc.bsky.social · 10/02/2026
📢 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
📢 Keynote reveal:
We’re excited to announce Prof. Dr. Oliver Stegle as a keynote speaker at HMC Conference 2026 – Metadata in Action!
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Stegle Lab @steglelab.bsky.social · 10/02/2026
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
doi.org
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Stegle Lab @steglelab.bsky.social · 02/02/2026
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...
embl.wd103.myworkdayjobs.com
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...
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Stegle Lab @steglelab.bsky.social · 20/01/2026
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...
drive.google.com
Alliance_project-outline Stegle Krijgsveld.pdf
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Stegle Lab @steglelab.bsky.social · 20/01/2026
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
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Stegle Lab @steglelab.bsky.social · 20/01/2026
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!).
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Stegle Lab @steglelab.bsky.social · 20/01/2026
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...
health-life-sciences.de
HEALTH + LIFE SCIENCE ALLIANCE | Interinstitutional Postdocs
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Stegle Lab @steglelab.bsky.social · 15/01/2026
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
elsa-ai.eu
ELSA Workshop “TrustworthyAI4Health: Toward Trustworthy AI Modeling for Computational Healthcare” – ELSA
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Stegle Lab @steglelab.bsky.social · 07/01/2026
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
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Stegle Lab @steglelab.bsky.social · 07/01/2026
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
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Stegle Lab @steglelab.bsky.social · 07/01/2026
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).
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Stegle Lab @steglelab.bsky.social · 07/01/2026
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.
interp-extrap-perturb.readthedocs.io
Interpretation, Extrapolation, and Perturbation of Single Cells — Interpretation, Extrapolation, and Perturbation of Single cells
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Stegle Lab @steglelab.bsky.social · 07/01/2026
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.
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Stegle Lab @steglelab.bsky.social · 07/01/2026
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)
rdcu.be
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...
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Stegle Lab @steglelab.bsky.social · 27/12/2025
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
biorxiv.org
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...
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Stegle Lab @steglelab.bsky.social · 27/12/2025
scPT-seq directly links genotype, expression, lineage & space in vivo. A powerful framework for functional genomics beyond indirect CRISPR readouts. 9/10
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Stegle Lab @steglelab.bsky.social · 27/12/2025
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
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Stegle Lab @steglelab.bsky.social · 27/12/2025
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
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Stegle Lab @steglelab.bsky.social · 27/12/2025
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
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