Oliver Stegle
@oliverstegle.bsky.social
Scientist at DKFZ and EMBL in Heidelberg, loving stats, genomics and genetics. @OliverStegle@genomic.social. For group news see @steglelab.bluesky.social
Our division is recruiting a PhD student through the Helmholtz Information and Data Science School for Health (HIDSS4Health). The supervision will be joint between me, @oliverstegle.bsky.social and @junyanlu.bsky.social. www.hidss4health.de/application/ → Project ID03 Deadline August 18
Application - Helmholtz Information & Data Science Academy
hidss4health.de
Our feature article: Interpretation, extrapolation and perturbation of single cells by @dbdimitrov.bsky.social, Stefan Schrod, @mrohbeck.bsky.social & @oliverstegle.bsky.social @steglelab.bsky.social go.nature.com/4csSbNq rdcu.be/feznS (Free to read)
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
Great opportunity! Bridge academia & industry. Join us on AI in genetics. Also for AI people with no (little) biology exposure.
Stegle Lab@steglelab.bsky.social · 5mo agoJoin 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...
Thank you. Looking forward, also to learn more about the HMC approach to metadata!
Helmholtz Metadata Collaboration@helmholtzhmc.bsky.social · 6mo ago📢 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
Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉 We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
Escape from X inactivation is directly modulated by Xist noncoding RNA
Nature Cell Biology - The authors show that increased Xist RNA levels can induce de novo silencing of genes that normally escape X inactivation. SPEN depletion prevents the silencing of escape...
rdcu.be
Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n
bioRxiv Genomics@biorxiv-genomic.bsky.social · 6mo agoMapping trans-eQTLs at single-cell resolution using Latent Interaction Variational Inference. https://www.biorxiv.org/content/10.64898/2026.02.04.703363v1
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
With @leopoldparts.bsky.social and @oliverstegle.bsky.social we comprehensively mapped CRISPRi responses in iPSCs identifying protein complexes as nexus for transcriptional changes and made a first step towards population-scale CRISPR screens to dissect genetic modulation of perturbation responses
I'm impressed by how far this model class has taken us—MOFA-FLEX may be the final iteration—a framework geared more towards generating models than being a standalone model itself. User-friendly, probabilistic programming rocks! We look forward to your feedback and experiences trying it out!
Stegle Lab@steglelab.bsky.social · 10mo agoAre 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
Are you an AI expert who wants to stay in academia and change the world by understanding the most complex things we know - living organisms? Want to lead your own group, based in Heidelberg DE, working language English? @embl.org is hiring in AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Group Leader – AI in Biology
Are you ready to lead groundbreaking research in AI for Biology? Join us at EMBL! We are seeking a visionary scientist to establish their own independent research group bridging innovations in machine...
embl.wd103.myworkdayjobs.com
If you want more information please contact @oliverstegle.bsky.social who is leading AI @ EMBL and please do forward this thread / websites to anyone who you think might be interested.
You are passionate about making data accessible? The Heidelberg Mannheim life science builds a data space - a major step for bridging basic science and translation. Two of more jobs to come. Technical lead and cloud engineer jobs.dkfz.de/en/jobs/1680... jobs.dkfz.de/en/jobs/1680...
Technical Lead for the "Health + Life Science Alliance Data Space"
jobs.dkfz.de
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
Postdoctoral Researcher in Computational Genetics
The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...
embl.wd103.myworkdayjobs.com
Are you based in the U.S. 🇺🇸 or Canada 🇨🇦 and thinking of doing research in Europe? ERC grants offer up to €4.5 million to support groundbreaking, investigator-driven frontier research in all fields. Watch the dedicated info session for researchers in your region👉 youtu.be/92QYink1Lik #ChooseEurope
ERC Grants: EU funding for your bottom-up research proposal (2025)
YouTube video by EURAXESS North America
youtu.be
European Research Council (ERC)@erc.europa.eu · last yr.Today, the ERC formally adopted a decision to increase its support for researchers moving to Europe. On top of its normal grants, the ERC offers 'start-up' funding to help PIs establish laboratories / research teams in Europe. This extra funding is now x2 (up to €2 million!) europa.eu/!6Vdgmp
Super happy and proud of this one. We and others have developed tools for dimensionality reduction for many years. MOFA (linear) and other non-linear generalisations, space/time. scDORI fuses this with GRN inference. It’s a nice and useful piece of software. Here applied to GBM biology.
Manu Saraswat@manusaraswat.bsky.social · last yr.🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇
Happy birthday! What a trajectory in just 3y. More exciting tools & packages and of course community.
scverse@scverse.bsky.social · last yr.scverse turns 3! What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community. From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together. Here’s to what’s next!
The next #ScienceatDKFZ event will take place on Monday, 12 May 2025, at 4 pm. In addition to the keynote lecture by Christoph Plass, there will be four 5-minute short talks by DKFZ junior scientists on recent highlight publications. ➡️ dkfz.de/en/news/even...
Our unit is connecting @dkfz.bsky.social, @uniheidelberg.bsky.social & @embl.org - @oliverstegle.bsky.social, @lena-maier-hein.bsky.social, @wkhuber.bsky.social, @brittavelten.bsky.social, Anna Kreshuk, Carsten Rother, Fred Hamprecht, Jan Korbel, Ullrich Köthe, Klaus Maier-Hein, Tilman Plehn, ...
“We all rely on science.” U.S. scientists are speaking out for scientific integrity and academic freedom. What they’re doing matters. We owe them our solidarity and a clear stand beside them. www.nytimes.com/2025/03/31/s...
Trump Administration Has Begun a War on Science, Researchers Say (Gift Article)
Nearly 2,000 scientists urged that Congress restore funding to federal agencies decimated by recent cuts.
nytimes.com
Are you a young researcher and want to access state-of-the-art technology? The Corporate Partnership Programme is your chance! 💥 CPP cover: 💡 opportunity to build new networks 💰 short-term fellows up to 4.000€ 🌍 eligible to stay at EMBL sites Apply until 31 March: www.embl.org/about/info/s...
Interview von Wolfgang Wick mit der Deutschen Welle zum Thema "Brain Drain" von Wissenschaflter*innen in den USA als Chance für Deutschland. Dieses Video ist nur auf deutsch erhältlich. youtu.be/0GtZ_lfL8Rc?...
Wie Europa von Trumps Krieg gegen die Wissenschaft profitieren könnte | DW Nachrichten
YouTube video by DW Deutsch
youtu.be
Interested in doing a sabbatical at EMBL, at one of its 6 sites in Barcelona, Cambridge, Grenoble, Hamburg, Heidelberg or Rome? Funding call with deadline 15 June, decisions in July. www.embl.org/about/info/s...
We’re thrilled to announce that the EMBL-EBI Thornton Building has been officially opened by Lord Vallance of Balham, the UK’s Minister for Science, Research and Innovation. We hope it will be a space where collaboration, translation, and science can thrive! 🌱
I could not really motivate myself to start properly on Bluesky following my departure from twitter. Maybe this picture is a good place to start. Antwerpen central station. What a building m!! Looking forward to www.vibconferences.be/events/revol...
Really great collab with @moritzgerstung.bsky.social and Dana Pe’er lab. Excited to hear what you all think. Cell segmentation is just hard… more to Come! Will also show a bit of it tomorrow at www.vibconferences.be/events/revol....
Revolutionizing Next-Generation Sequencing (6th edition)
19-21 March 2025, Antwerp, Belgium A VIB Tools and Technologies conference
vibconferences.be
Stegle Lab@steglelab.bsky.social · last yr.1/ New preprint! 🍳 @elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins! doi.org/10.1101/2025...
Next up: Melissa Sanabria on LLMs for genomic data. What is the best vocabulary to tokenise DNA sequences? #EESAIBio.
New Symposium on AI and Biology starting now! #EMBL #EESAIBio. www.embl.org/about/info/c...
