Thanks to team for wonderful lab xmas party yesterday! 🎄🎅🏼 Besides Feuerzangenbowle (=mulled wine^2) we had this funny guess-the-paper from Santa's crazy review. Not sure you can guess the paper 📝, but I loved ~summary "Benchmarking the benchmark of benchmarking benchmarks."😅

🎄 We’re hiring in Health AI at @HelmholtzMunich! 🔹 PIs in Health AI/AI Foundations 🔹 Health AI Fellows 🔹 Clinical AI Consultants Apply👇 PIs: jobs.helmholtz-muenchen.de/jobposting/8... Fellows: jobs.helmholtz-muenchen.de/jobposting/7... Consult: jobs.helmholtz-muenchen.de/jobposting/c...

🚀 New preprint! The Human Cytokine Dictionary - 9.7M cells, 12 donors, 90 cytokines - our largest human single-cell perturbation atlas yet. Users can map cytokine activity in their own data. Huge thanks to Lukas, Sören, Larsen, Parse Bio & Seelig lab! 🔗 www.biorxiv.org/content/10.6...

Nature Methods names AI agents a “Method to Watch”! We've started building active-learning loops with perturbation models, where AI proposes experiments & data closes loop. Supplying such models to agents could transform exp design into theory search. www.nature.com/articles/s41...

Excited to share new preprint led by Sergio Salas on “unassigned RNAs” in imaging-based spatial transcriptomics. Across technologies, 30-40% of transcripts fall outside segmentation, & many show structured, biologically meaningful extrasomatic patterns. 📄 www.biorxiv.org/content/10.6...

🚀 Excited to share our preprint scConcept: a contrastive pretraining framework for technology-agnostic single-cell representations. We move beyond reconstruction to learn rich, cell-level embeddings for diverse omics. 📘 www.biorxiv.org/content/10.1...

Breaking down walls in #PrecisionHealth at #FallingWalls 2025! Great exchange with Frank Laukien, Caroline Gubser-Keller, Eicke Latz & Steve Quake on how AI & molecular analytics reshape medicine. Our goal: virtual twin cells, tissues & patients. #AIinMedicine #HelmholtzMunich

🚀 Prophet v3 is out! AI that predicts how cells respond to genetic & chemical perturbations across readouts. Now scales to 1.9 M molecules + in vitro validation of melanoma-specific hits 🧬💊 📄 biorxiv.org/content/10.1... #AI #Biology #DeepLearning

EU commissioner Henna Virkkunen officially launching EU‘s RAISE project - its Resource for AI Science in Europe at AIS25 in Copenhagen. includes training programs, data hubs, funding and compute. Exciting & important for Europe and beyond. 🇪🇺

Munich is now the #2 AI ecosystem in Europe (after Paris) and #11 globally, per Dealroom’s Global Tech Ecosystem Index 2025! 🇩🇪🤖🇫🇷 Proud of the growing strength of the Bavarian AI ecosystem 👉 baiosphere.org �� dealroom.co/tech-ecosystem-index-2025�5#Munich #baiosphereiosphere

🔗 To the original publication in Nature Methods: t1p.de/ba2gx @fabiantheis.bsky.social @comphealthmunich.bsky.social

🎃 Happy Halloween from our Lab! 👻🧬 No bad computational tricks — only treats! 🧫💻✨

Looking for a PhD/postdoc position in Cambridge UK in comp bio? Check out Hana Aliee's new lab at CRUK: www.cruk.cam.ac.uk/research-gro...

🧬 Excited to share Nicheformer out now in Nature Methods! A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization. Led by Ale Tejada & Anna Schaar 👏 👉 www.nature.com/articles/s41...

At the Staatskanzlei Munich for the State Reception celebrating Bavaria’s Excellence Clusters — great to see so much scientific excellence and innovation recognized and supported across disciplines. 🚀🇩🇪 #Wissenschaft #Innovation #Bayern

Our preprint on scPortrait is out! We built a framework + format to turn microscopy into standardized single-cell image datasets. #scPortrait scales >100M cells, integrates with @scverse.bsky.social, & enables cross-modality modeling from morphology to transcriptomics doi.org/10.1101/2025...

✨ Prof. Eric Topol visited #HelmholtzMunich for a roundtable on the future of #AI in healthcare. The discussion focused on the concept of the #VirtualHuman. 👉Read more: t1p.de/5wthc #AIinMedicine #DigitalHuman #PrecisionMedicine

Björn Schuller from TUM and Imperial talking about deep learning on mobile sensor data at scale. Wonder how and when we get all these scales together. #BavarianAcademy #MedicalAIConference

Eric Topol giving evening keynote at our Bavarian Conference on AI in medicine, amongst other on AI for prevention and super aging. A true visionary and communicator! see eg erictopol.substack.com/p/dawn-of-a-... @eriktopol

Inspiring evening w/ Eric Topol, Matthias Tschöp & Markus Schwaiger. Key message: unite scientists and data across institutions to make AI medicine real — starting with prevention. 🧬🤝 Excited for the Bavarian AI in Medicine Conference tomorrow.

Looking fwd to Bavarian Conference on AI in Medicine (Oct 27–28) in Munich: events.hifis.net/event/2048 with Eric Topol, Mihaela van der Schaar, & Islem Rekik. Plus prologue with @erictopol at Helmholtz Munich on monday morning. Let’s discuss where AI can really impact medicine. 💡

🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): www.science.org/doi/10.1126/... We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁

Our lab together with the Lücken lab is in the mountains for our annual hackathon & retreat ⛰️💻 A great mix of science and community: new project ideas, evening coding, creative drawing, and a group hike. Inspiring energy & fresh thinking, truly grateful for this awesome team!

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights. 🔗 www.biorxiv.org/content/10.1...

Excited to speak today at the EC’s R&I Community event on RAISE – Building the Resource for AI Science in Europe. We’ll discuss how pooling compute, data, talent & funding can supercharge AI-driven discovery across life sciences & health. 👉 stream: research-innovation-community.ec.europa.eu

2nd day of our DLD Baiosphere conference starting out w aim to ‘put on some fairy dust’ (Yossi Vardi’s words) - w supermotivating Bohemian Rhapsody flashmob vid, watch it will make your day ☺️ youtu.be/jO2R_35HhiY

Excited that our DLD Baiosphere conference on AI is starting now - with major political presence from Bavaria & great talks/panels from science and industry! MP Söder with strong commitment on academic freedom & local strength in AI to attract talents. 🚀https://dld-conference.com

New paper in @ScienceMagazine with Schoof & Porse labs: We chart early human hematopoiesis using single-cell proteomics, and amongst others developed a dynamic model linking RNA to protein levels, explaining more proteomic variation. 📄 www.science.org/doi/10.1126/...

Back from the SolvAI Retreat 2025 in Nice — amazing discussions on AI in science. Key themes: LMs alone won’t get us to scientific discovery, what makes a theory, and how AI can help us build them. Thanks to Eric Xing & Yann LeCun for organizing!

So excited to see it out in @science.org. See details below in the 🧵 from stellar former PhD student @bfurtwa.bsky.social. Many thanks to all involved, especially Blueskyless Nil Uresin and Sabrina Richer and my co-PIs @fabiantheis.bsky.social and @erwinschoof.bsky.social

🚀 NSF just announced a $100M investment in National AI Research Institutes, with medicine & health applications listed first among priority areas, highlighting how biomedical impact continues to lead innovation and real-world benefit! www.nsf.gov/news/nsf-ann... 👩⚕️🔬 #AI #Health

🚀 Exciting opportunity for scientists in the Bavarian AI ecosystem @bAIosphere! Host your funded retreat or workshop at the beautiful, remote Speinshart Scientific Center for AI & SuperTech🤖. 👉 baiosphere.org/baiosphere-s... 👉 www.speinshart.ai #AI #Bavaria #ScienceCommunity

Great to host Eric Xing, President & University Professor at MBZUAI, together with Dekyi Liang, Chief of Staff, at our Helmholtz Computational Health Center last Friday 🤖. Inspiring talk on “AI-driven Digital Organism” and engaging discussions with colleagues & PIs 🧬.

Very honored to receive the 2025 ISCB Innovator Award at #ISMBECCB2025 and present our lab’s journey—from mapping cells to modeling their future. Thanks to my amazing team and collaborators—this is our award! 🙌 📽️ Keynote: Atlases, AI & virtual cells 📝 doi.org/10.1093/bioi...

Three #ERC Proof of Concept Grants for #HelmholtzMunich 🚀 Projects by Marcus Conrad, Fabian Theis & André C. Stiel target cancer, AI-guided drug delivery & chip-based diagnostics. 👉 t1p.de/hz9x3 @erc.europa.eu @fabiantheis.bsky.social

Laura Martens doing great job at presenting our work on deconvolution of spatial ATAC data at #ISMBECCB2025 at Liverpool - essentially: transcriptomic methods work here, too. academic.oup.com/bioinformati...

Interesting: www.nature.com/articles/d41... - low quality papers linking some seemingly random phenotypes eg in UKBiobank, "flooding" the literature. Exploring all possible combinatorial possibilities of phenotype combinations sounds like a science business model now...

Helmholtz Computational Health Center summer party! 🌞🎉 great people, great energy, and a reminder that science thrives with community! #TeamScience

Thrilled to collaborate with Mathew Garnett @Sanger and Parse Biosciences on the new Cancer Plasticity Atlas – a hugely exciting single cell genomics resource to decode tumor adaptation. 🔗 helmholtz-munich.de/en/newsroom/news-all/artikel/cancer-plasticity-atlas-to-improve-cancer-therapies

Join us for a series of presentations from leading data science experts, including @francescafinotello.bsky.social, @dominicgrun.bsky.social, Johanna Klughammer, Malte Lücken, @fabiantheis.bsky.social and @jwrth.genomic.social.ap.brid.gy.

🔬API-first feature extraction for image-based profiling workflows If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle. 1/6

🚀 Ewa Szczurek kicking off the AI for Health Symposium 2025 at Helmholtz Munich today! Excited to listen to local and international experts on how generative AI is transforming molecule discovery and health. 🌟 events.hifis.net/event/2015 #AIforHealth #GenAI #Helmholtz

🏆 Helmholtz Munich wins the #m4Award2025 for SYNTRA, an #AI-powered #RNA delivery project. The pre-seed prize supports spin-offs in Bavaria. SYNTRA aims to safely deliver RNA to target cells, enabling new therapies for genetic & other diseases. 👉 t1p.de/6fyup @fabiantheis.bsky.social #BioM

🚀 Yesterday marked kickoff of the *M1 Munich Medicine Alliance* – uniting LMU, TUM, and Helmholtz Munich to build Germany’s leading medical innovation hub. Major step twds translational excellence, AI-powered health, & better patient outcomes. Great! 🔗 m1.bayern

New OpenProblems paper out! 📝 Led by Malte Lücken with Smita Krishnaswamy, we present openproblems.bio – a community-driven platform benchmarking single-cell analysis methods. Excited about transparent, evolving best practices for the field! 🔗 www.nature.com/articles/s41...

Cancer Plasticity Atlas To Improve Cancer Therapies #HelmholtzMunich joins @sangerinstitute.bsky.social & @parse.bsky.social to build the Cancer Plasticity Atlas, using #AI & single-cell data to model therapy response. 👉 t1p.de/13ifi @fabiantheis.bsky.social @mgarnett.bsky.social #CancerResearch

NetworkVI is a group effort by @juliusuzb.bsky.social, Luis Herrmann, Khue Nguyen, supervised by @fabiantheis.bsky.social & Benjamin Wild & Roland Eils at @bihatcharite.bsky.social and @www.helmholtz-munich.de‬. Code: github.com/LArnoldt/networkVI 🧠 Open-source & ready to use!

Grateful to all co-authors and collaborators for their contributions and insight throughout this project. Fabian Theis @fabiantheis.bsky.social, Malte Luecken, Muzzlifah Haniffa @mhaniffa.bsky.social, and Antony Rose.

Defining and benchmarking open problems in single-cell analysis - @krishnaswamylab.bsky.social @fabiantheis.bsky.social bit.ly/4l8dsiF

@OpenAI opening its first German office in Munich. Exciting discussion & vision from Nick Turley, chatgpt lead and original Munich guy, but also politics @Markus_Soeder. Looking fwd to seeing impact in science directly here.