Stegle Lab
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steglelab.bsky.social
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/
Pinned
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
February 10, 2026 at 11:46 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
February 10, 2026 at 8:59 AM
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...
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
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 SCIENCE ALLIANCE | Interinstitutional Postdocs
www.health-life-sciences.de
January 20, 2026 at 9:43 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
January 15, 2026 at 10:09 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)
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
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
December 27, 2025 at 4:13 PM
We are looking for a Software Developer to work on R/Python interoperability for single-cell and spatial omics methods.

🔗 Apply here: jobs.dkfz.de/en/jobs/1683...
Software Developer - Interoperability for Single-Cell and Spatial Omics Methods
jobs.dkfz.de
December 27, 2025 at 3:50 PM
We’re excited to announce the "Toward Trustworthy AI Modeling for Computational Healthcare" @elsa-ai.eu workshop, a one-day in-person event focused on building private, fair, robust, reliable, and accountable AI systems for healthcare. Register now.

📅 March 9, 2026
📍 EMBL, Heidelberg, Germany
Registrations just opened for the workshop “TrustworthyAI4Health: Toward #TrustworthyAI Modeling for Computational #Healthcare”!🔥

Join us on March 9, 2026, to advance private, fair, robust, reliable, and accountable AI models for healthcare applications.

elsa-ai.eu/elsa-worksho...
December 19, 2025 at 1:42 PM
Meet Hendrik Mehrtens who recently joined our lab as a PhD student - shared with @mlolab.bsky.social 👋

Hendrik’s research focuses on reliable machine learning methods integrating large-scale EHR data with multimodal data like genomics data, with a focus on causality and uncertainty estimation.
December 5, 2025 at 3:41 PM
Reposted by Stegle Lab
Claudia Feng's Ph.D work is now out, co-led with @brittavelten.bsky.social and @steglelab.bsky.social . Large-scale CRISPRi perturbations in genetically heterogenous iPSC lines, with single cell readout - enjoy :)
December 3, 2025 at 11:04 AM
Back from #scverse25 and feeling inspired by what @scverse.bsky.social has achieved over the last years. Impressive tools, a vibrant community and we even had a reunion with our two alumni Danila and Max Frank.

We also presented our latest findings from the lab 👇
November 25, 2025 at 9:01 AM
Reposted by Stegle Lab
The ELLIS Society welcomes its new Board. As the primary decision-making body, it will play a vital role in shaping the future of ELLIS and advancing #AI and #MachineLearning research across Europe in a time of global change.

Read the full article: ellis.eu/news/ellis-s...
October 27, 2025 at 9:15 AM
Welcome to our team, Gesa Voigt! 👋

During her molecular biology studies, Gesa developed an interest in applying mathematics and ML to understand complex biological systems. Her PhD research will focus on inferring GRNs by integrating insights from population genetics and genetic perturbation data.
November 12, 2025 at 12:30 PM
Please join me in welcoming Stefanie Mantz to our lab! 👋

Steffi joins us as a PhD student after completing her Master’s at Heidelberg University. She will explore gene regulation and cell differentiation using organoid models and is excited to analyze these complex datasets and develop ML methods.
November 10, 2025 at 12:30 PM
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!

Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
November 7, 2025 at 10:29 AM
Reposted by Stegle Lab
Thank you to everyone who joined the Life Science Thematic Workshop at the AI in Science Summit in Copenhagen.

Led by EMBL’s Oliver Stegle and Anna Kreshuk, the workshop united researchers and AI experts to explore how advanced computational approaches are shaping the future of life sciences.

#ai
November 4, 2025 at 12:47 PM
Looking forward to this collab with @moritzmall.bsky.social and Barbara Treutlein!

We’ll generate high-throughput multi-modal CRISPR data on ASD risk genes in 🧠 organoids & assembloids, and build an ML model of gene regulation dynamics to analyze the data and enable future in silico experiments.
Presenting recipients of our 2025 Stimulator Grant:
👉TACTICS: Thalamocortical Assembloids and Computational Tools for Investigating Cellular Signatures in #Autism.
🧠How do autism-linked mutations disrupt early brain development? @moritzmall.bsky.social @steglelab.bsky.social
@dkfz.bsky.social
October 14, 2025 at 11:42 AM
Do you want to link genomic variants to functional gene expression - cell by cell?
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
embl.org EMBL @embl.org · Oct 10
EMBL scientists have created a more sensitive single-cell sequencing tool for genomic variants and RNA in the same single cell.

Known as SDR-seq, the tool has unprecedented scale, precision, and speed to characterise variants and link them to functions and disease.

www.embl.org/news/science...
New tool offers single-cell study of specific genetic variants | EMBL
Scientists developed a more sensitive single-cell sequencing tool linking genomic variants & RNA in the same cell uncover links to disease.
www.embl.org
October 10, 2025 at 2:42 PM
Don’t miss Manu’s poster on DeepGenoXcan, our new personalized and interpretable sequence-to-expression model, at #ASHG2025!

📅 October 16, 2:30pm-4:30pm
📍 Poster 1007T
Excited to be at #ASHG2025 in Boston next week. On Thursday, I will be presenting a poster (1007T) on our latest work on Personalised sequence to expression modelling. Looking forward to meeting new folks and reconnecting with old friends and colleagues.
October 10, 2025 at 1:35 PM
Super excited for the 2nd edition of the #scverse conference!
A fantastic opportunity to showcase and discover innovative data frameworks for #singlecell analysis, and to meet the developers behind the scverse ecosystem. Looking forward to connecting with the community!
Register now! 👇
August 28, 2025 at 3:59 PM
A scalable framework enabling the induction and spatial genotyping ➡ phenotyping of hundreds of tumors in mouse liver. #CHOCOLAT-G2P

Check out the publication for the nuts and bolts of 🍫-G2P: doi.org/10.1038/s415...
August 7, 2025 at 7:27 AM
We're seeking a PhD student passionate about ML, biology, and driving impact in healthcare!

You'll be working on multi-omics factorization models for personalized medicine, co-supervised by @junyanlu.bsky.social.

👉 Project: www.helmholtz.de/assets/hidss...
✍️ Apply: hidss4health.de/application
Application - Helmholtz Information & Data Science Academy
hidss4health.de
August 5, 2025 at 8:08 AM
Reposted by Stegle Lab
🌐 EMBL’s new initiative is set to transform life science research through full AI integration – from genomics to drug discovery.

💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.

www.embl.org/news/connect...
August 1, 2025 at 7:15 AM
Reposted by Stegle Lab
To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Group Leader - Genome Biology Unit
Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...
embl.wd103.myworkdayjobs.com
July 30, 2025 at 1:41 PM