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 · 4mo ago

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...

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 ago

Mapping 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 · 9mo ago

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

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!

This week's genome editing triumph is a big deal. Here's why erictopol.substack.com/p/the-first-...

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, ...

Start your own group at DKFZ! jobs.dkfz.de/en/jobs/1677...

Head of an independent Junior Research Group with Tenure Option at the German Cancer Research Center (DKFZ)

jobs.dkfz.de

“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

Reverse brain drain? But yes, science in Europe is great!

Justin Crocker@justinmcrocker.bsky.social · last yr.

Judging by the new round of PhD student applicants to @embl.org the brain drain has started. DM me if you have questions about moving to Europe.

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...