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.

📢PUBLISHED @naturegenet.bsky.social ✨Don't miss this Perspective on the application of causal machine learning to single-cell genomics and its associated challenges. By @fabiantheis.bsky.social and colleagues! ⬇️ www.nature.com/articles/s41...

Yay, we built a thing! With @dominik1klein.bsky.social Daniil, Aviv Regev, Barbara Treutlein @graycamplab.bsky.social @fabiantheis.bsky.social we use flow matching to enable generalised sc phenotype modeling. From cytokine screens to fate programming and organoid engineering tinyurl.com/3xhju7db

Learned a lot working with Jonas Fleck, Daniil Bobrovskiy, Dominik Klein, Barbara Treutlein and @fabiantheis.bsky.social on CellFlow: generative single-cell phenotype modeling with flow matching. Virtual protocol screening is particularly innovative!

Integrated Organoid Atlas benchmarks new protocols, even more impressive as a Highly Variable Cohort for comparison against perturbation and disease models: nature.com/articles/s41... Lead by @quanxu.bsky.social, in collaboration with Lennard Halle and @fabiantheis.bsky.social

Mapping the Future of Organoids Researchers at #HelmholtzMunich, with Roche's IHB & ETH, built detailed atlases of #brain, #gut & #lung #organoids - tiny stem-cell-grown organ models. 👉 t1p.de/avhdz #HumanCellAtlas @ethz.ch @fabiantheis.bsky.social @quanxu.bsky.social @graycamplab.bsky.social

What makes the Computational Health Center unique? It thrives within a dynamic ecosystem of academia, industry & biotech. Focused on AI-driven health solutions, it plays a key role in accelerating the global application of #PrecisionMedicine. 👉 t1p.de/yg4od @fabiantheis.bsky.social #AIinHealth

This Registered Report from @fabiantheis.bsky.social and colleagues evaluates feature selection methods and provides guidance on how feature selections impact scRNA-seq integration analysis. www.nature.com/articles/s41...

🧬If you work with @10xgenomics.bsky.social Xenium, this might be of your interest. Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social www.nature.com/articles/s41...

We asked J. Moffitt, M. Li, Q., K. Kanemaru, S. Teichmann, D. Dar, S. Itzkovitz, R. Vento-Tormo, @ltkagohara.bsky.social @itaiyanai.bsky.social @fertiglab.bsky.social @fabiantheis.bsky.social about bottlenecks facing Spatial Transcriptomics www.cell.com/cell-systems/abstract/S2405-4712(25)00033-X

🎉 Scanpy 1.11.0 is out! 🎉 just after reaching 2000 stars on GitHub! - sc.pp.sample replaces subsample with many new features - Sparse Dask support pca - session-info2 package for more reproducible notebooks See the release notes:

Addressing Bias in Machine Learning for Equitable Healthcare 👉Learn more: t1p.de/7t8fp @theresawillem.bsky.social @fabiantheis.bsky.social @shitovhappens.bsky.social @marie--p.bsky.social @alenabuyx.bsky.social #AI #healthcare #MachineLearning #bias

‚Foundation models for biology‘ are one of 6 techs to watch in 2025 according to @Nature. Agreed, but not sure yet how to evaluate at scale. ie what is ‚general biological intelligence’? www.nature.com/articles/d41...

I'm excited about a meeting on RNA + AI together with @quaidmorris.bsky.social and @hagentilgner.bsky.social in Ascona, Ticino on May 4-8. We have a great line-up of speakers and room for you to present your work. Please join us if you are into RNA & AI. Registration open www.rna-ai.org.

Fabian Theis and his team tested self-supervised #learning as a promising approach for analyzing and interpreting huge amounts of #data, such as millions of individual cells: go.tum.de/217457 #biomedicine #machinelearning @www.helmholtz-munich.de @fabiantheis.bsky.social 📷iStock/Amiak

Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep

#AI in Biomedicine: Transforming Cell Research Researchers at #HelmholtzMunich & TUM are using #MachineLearning, including self-supervised learning, to analyze over 20 million cells efficiently. t1p.de/9gt9r @fabiantheis.bsky.social

Exciting new tool to make the most out of multimodal single-cell data from our friends and long-term collaborators of the @fabian_theis lab - check it out, it works beautifully and really makes sense out of your complex data! 👇👍😉

Excited to see Moscot (moscot-tools.org) published in @Nature! We scaled Optimal Transport (OT) in single-cell genomics & added multimodality together with spatiotemporal trajectory inference, finding exciting new biology in the pancreas! 🚀 Read at www.nature.com/articles/s41...

Our paper on Self-Supervised Learning in Single-Cell Genomics is out in Nature Portfolio Machine Intelligence! 🙌 🧬🤖 Big thank you to my co-authors Mojtaba Bahrami, Yufan Xia, @davidsebfischer.bsky.social, and @fabiantheis.bsky.social . 👏 nature.com/articles/s42...

AI in Cell Research: Unveiling Organ Development #Moscot, a groundbreaking #AI tool developed by an international team led by #HelmholtzMunich, tracks cells in real time, revealing how organs like the #pancreas form. t1p.de/viil5 @fabiantheis.bsky.social @nature.com

Delineating the effective use of self-supervised learning in single-cell genomics www.nature.com/articles/s42... @fabiantheis.bsky.social

What was your favorite science entertainment read this holiday? Mine was ‘Forever Young’ by Maxim Leo - a short, well researched novel on what happens after rejuvenation & longevity therapy actually works. Fun read!

Fun fact: there’s no reason to ever underline text, it’s just not pretty.

If diving into scientific papers isn’t on your pre-Christmas to-do list, @spiegel.de has you covered! 📰 They featured our Neural Organoid Atlas in a piece on the Human Cell Atlas and related advancements in machine learning. 🤖🧬 It’s a great overview of this exciting field and the work behind it.