Posts on X

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! 🙌 📝 doi.org/10.1093/bioinf…

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/bioinformatics…

Interesting: nature.com/articles/d4158… - 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 and resistance. 🔗 helmholtz-munich.de/en/newsroom/ne… #CancerAI #Plasticity #Atlas

🚀 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

🚀 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! 🔗 nature.com/articles/s4158…

1/ Excited to share CellFlow, a new approach for complex perturbation modeling in single-cell genomics based on flow matching. From cytokine screens to cell fate and organoid engineering, we show CellFlow’s broad power across many diverse tasks. 👉 Paper: biorxiv.org/content/10.110…

‚Occam’s razor has been thrown away. We’re living in the age of Occam’s chain saw, when the preferred answer is the one that makes the loudest noise and generates the most debris.‘ (from @nytimes opinion) 🪚

Steffen Schneider @CompHealthMuc presenting his AI education program ‘KI macht Schule’ (AI ‘makes’ school) at our department townhall today - exciting and already impactful effort!

Exciting @GermanStemCell workshop on computational approaches in single cell genomics in stem cell research! 🧬🔬 With Sara and Tim, two trainer from the lab, this’ll be fun! More info & registration here: gscn.org/conferences-ev… 🌟

Exciting job opportunity!🚨 Join our lab at Helmholtz Munich as a Postdoc to develop cutting-edge AI for single cell analysis & drug discovery targeting neuroinflammatory diseases 🧠, collaborating closely with our partners at @UniofOxford! Apply here👇 jobs.helmholtz-muenchen.de/jobposting/7aa…

1/: Excited to share our new study led by Luke Zappia on feature selection methods for single-cell RNA-seq data, now published @naturemethods ! We explore how choosing features impacts reference atlases & downstream analyses. 📊📚 nature.com/articles/s4159…

Interested in exploring @vevo_ai’s massive Tahoe-100M single-cell perturbation dataset? #Scanpy now supports out-of-core analysis, powered by Dask—allowing you to seamlessly work with a single huge AnnData object without loading everything into memory. 🔗 theislab.github.io/vevo_Tahoe_100…

GIF, plays on X

1/ „What is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling?" @CellSystemsCP asked a few of us for comments on this, I think quite cool read here at sciencedirect.com/science/articl…

1/ When talking about virtual cells, we usually mean large data-driven cell representation models. I still do like GRN representations and their extreme usefulness for true out-of-distribution predictions. Many ways to get to them, eg we recently proposed regvelo to combine.

‚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’? nature.com/articles/d4158…

At podium discussion w theologist, being asked about AGI challenging human soul: ‚From god‘s perspective, human beings are artificial intelligences, works of art.‘ Love it! 🎨

Grand opening of the AI Hub at LMU, w Minister @FabianMehring summarizing Bavaria’s substantial investments into AI over the years. baiosphere.org

DeepSeek isn’t just fun to use (thanks @ollama) - it’s also shaking up science, since it lets us see inside. More @Nature nature.com/articles/d4158…

Highly recommend trying out @ollama's DeepSeek reasoning model, runs on your laptop! 🧠 The thinking process is fascinating—perfect for exploring structured, logical reasoning in action. And nice&cute to see how it argues w itself. #AI #DeepSeek #ReasoningModels

1/ Excited to see 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 nature.com/articles/s4158…

Colin Jarvis @OpenAI presenting @DLDConference about recent advances in LLM reasoning and multimodality. Smaller models but longer thinking helps improve quality.

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 @altoslab @calico kiwi-verlag.de/verlag/rights/…

🚨 We're hiring! 🚨
Join our team as a Lab & Science Manager for the Theis lab! 🧬🧪 Help drive cutting-edge research, manage lab operations, and enable scientific excellence. 🌟 📍 Munich, Germany
🔗 Apply here: jobs.helmholtz-muenchen.de/jobposting/56d…
#ScienceJobs #LabManagement #Helmholtz

Excited to share our atlas build&use guide, out @naturemethods today. Led by @KHrovatin & @SikkemaLisa w @MDLuecken, our review highlights best practices for building, sharing, and leveraging atlases to unlock new biological discoveries. 🌍@humancellatlas nature.com/articles/s4159…

1/🚀 Excited to share RegVelo, our new computational model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.110…

scRNA-seq data sets exploding in number and size - check out scanpy & anndata for >1b cells: new experimental update includes APIs for scaling with dask from anndata, integrated with lots of scanpy and rapids-singlecell functions. gist.github.com/ilan-gold/9880…

1/2 🚀 Discrete Optimal Transport (OT) has proved useful in a wide variety of tasks in single-cell genomics, see e.g. moscot-tools.org. Can we combine this powerful concept this with novel generative models? 🤔 🌟 Enter GENOT: Generative Entropic Neural OT.