iiinova — where your digital self keeps evolving

Fabian Theis @fabiantheis.bsky.social · 09/06/2026

Excited to kick off #HAICON26 today! 🚀🤖 More than 600 participants joining us to explore how AI is transforming science and accelerating discovery. Great energy, great people, and an exciting program ahead. 👉 haicon.cc #AIforScience #HAICON26

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Reposted by Fabian Theis

Mann Lab @mannlab.bsky.social · 28/05/2026

1/5 Cell identity is written in the proteome, not in the DNA, and not always in the RNA. Out on bioRxiv today: The first cell type-resolved, MS-based proteomic atlas of the human body. www.biorxiv.org/content/10.6...

biorxiv.org

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Fabian Theis @fabiantheis.bsky.social · 27/05/2026

Beautiful short Nature Methods N&V “Teaching an old dog new cells” led by J Linder & D Kelley. Also on scooby, pushing seq2func models toward true cell-state–specific reg modeling 🧬 Fitting disc here at CSHL with Anshul & others on this next frontier www.nature.com/articles/s41...

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Aayush Grover @aayushgrover.bsky.social · 23/05/2026

Excited to share that UniversalEPI is officially published in @narjournal.bsky.social! 🚀 Check out the final paper and use the model here: 📄 Paper: academic.oup.com/nar/article/... 💻 Code: github.com/BoevaLab/Uni... (1/3) 🧵

academic.oup.com

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Fabian Theis @fabiantheis.bsky.social · 19/05/2026

50 today 🎉 Feeling a tad older, but mostly very grateful: to family, friends, colleagues, collaborators, and students for the journey so far! Huge thanks to my department for the amazing surprise reception today. You certainly know how to celebrate science & aging in style 😄🚀

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Fabian Theis @fabiantheis.bsky.social · 13/05/2026

Enjoying inspiring discussions with colleagues & friends at the GRC Single Cell Genomics conference in Les Diablerets, surrounded by an awe-inspiring mountain landscape. Special setting for maybe grand ideas!

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Fabian Theis @fabiantheis.bsky.social · 12/05/2026

Excited to share our RegVelo paper in Cell www.cell.com/cell/fulltex... We unify RNA velocity + GRNs into one model → better OOD prediction of perturbations (e.g. gene KOs), with examples incl. neural crest KO predictions 🔬 Big thanks to W Wang, Z Hu & T Sauka-Spengler 🙏

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Fabian Theis @fabiantheis.bsky.social · 01/04/2026

New preprint with Garnett lab 🚀: from descriptive → causal single-cell atlases in CRC.We build the largest CRC atlas (>300 pts, 1.5M cells) using continual learning, and link cell states to causal drivers via Tahoe-100M, validated in organoids! www.biorxiv.org/content/10.6...

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Fabian Theis @fabiantheis.bsky.social · 27/03/2026

Excited to share our cross-species PDAC atlas preprint led by D Lucarelli & S Parikh in collab with D Saur: www.biorxiv.org/content/10.6... 1.6M single cells (human + mouse) to quantify how well models capture disease 🧬 Core programs are conserved, even rare immune pops clearly aligned.

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Fabian Theis @fabiantheis.bsky.social · 24/03/2026

Great to be at Roche’s new Institute for Human Biology (IHB) in Basel. Spoke on 'virtual organoids' & predictive models. Inspiring talks from Paola Arlotta, Amy Shyer & Mark Fishman. Exciting convergence of biology, engineering & AI - congrats to Roche on this bold initiative!

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Fabian Theis @fabiantheis.bsky.social · 24/03/2026

At Novartis Campus Basel yesterday for our 2nd Helmholtz Munich × Novartis workshop on advancing AI + multi-modal kidney disease research, from cross-species atlases to targets. Thanks Caroline Gubser-Keller & team for great discussions! www.helmholtz-munich.de/en/icb/news-...

helmholtz-munich.de

Helmholtz Munich Launches Collaboration on AI-Driven Kidney Disease Research

Helmholtz Munich and Novartis Biomedical Research are launching a four-year collaboration to advance kidney disease research. Starting in early 2026, the partnership will work to develop an…

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Fabian Theis @fabiantheis.bsky.social · 17/03/2026

Excited to share new preprint with NVIDIA on GPU-accelerated single-cell analysis 🚀 rapids-singlecell brings native GPU support to scverse/AnnData: hours → seconds (1M cells: ~52m → ~25s), scaling to 100M cells. Huge thanks to Severin Dicks 🙌 📄 arxiv.org/abs/2603.02402

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Fabian Theis @fabiantheis.bsky.social · 10/03/2026

🚀 New in Communications Biology: Generative models of cell dynamics - from Neural ODEs to Flow Matching www.nature.com/articles/s42... We discuss modeling single-cell dynamics beyond snapshots: from cont-time Neural ODEs to simulation-free flow matching for scalable pop modeling.

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Fabian Theis @fabiantheis.bsky.social · 05/03/2026

Hazel Brugger moderating Google Berlin AI Center Evening party - not just entertaining but compelling w eg Minister D Bär on Germany‘s High Tech Agenda pushing Ai for health, biotech & energy!

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Fabian Theis @fabiantheis.bsky.social · 05/03/2026

🚀 Opening of the Google AI Center Berlin - a strong signal for AI in Europe. Great to join Minister K Wildberger, Mayor K Wegner, Yossi Matias and others to discuss AI in science. Proud that our Helmholtz Munich & TUM teams presented joint work on AI for health!

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Fabian Theis @fabiantheis.bsky.social · 03/03/2026

🗞️ At 'Digitalgipfel' of Süddeutsche Zeitung: www.sz-gipfel.de/digitalgipfel Germany's Digit. Minister Karsten Wildberger just outlined plans for unified citizen app & digital wallet 🇩🇪, finally! Me contributing to “KI konkret”, about how AI revolution is well underway in biomed.

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Reposted by Fabian Theis

Vladimir Shitov @shitovhappens.bsky.social · 26/02/2026

How to learn gene regulation patterns from multimodal single-cell data? To answer this question, we at OpenProblems organised the Kaggle competition on modality prediction. It ran back in 2022 but still remains the world's largest competition in the single-cell field. 1/17

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Fabian Theis @fabiantheis.bsky.social · 27/02/2026

At the 132nd Internat. Titisee Conference on Biology 2.0: The AI Revolution in Biology & Medicine From sequence→function models 🧬 to protein & generative structure models 🧪 to AI of cell states & perturbations 🧫 Great science, great friends, beautiful lake. Thanks @BIFonds!

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Reposted by Fabian Theis

Cell Press Events @cellpressevents.bsky.social · 25/02/2026

Join us at the #CellPressSymposia: Decoding cellular complexity: Single cell biology in the era of AI, Dec 2–4, 2026, Munich, Germany, in partnership with @helmholtzmunich.bsky.social. #CPSsinglecellbiology2026 @ethz.ch.bsky.social dlvr.it/TR8Rw9

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Fabian Theis @fabiantheis.bsky.social · 24/02/2026

Join us at Cell Symposia: Single-Cell Biology in the Era of AI (Dec 2–4, 2026, Munich) 🇩🇪 From multi-omics to AI-driven models of cellular dynamics — an exciting lineup across experimental & computational biology. Hope to see you there! 🔗 www.cell-symposia.com/single-cell-...

cell-symposia.com

Home – Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI

Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI

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Fabian Theis @fabiantheis.bsky.social · 24/02/2026

Looking forward to tonight’s Synapse Munich fireside chat 🔥 Great to connect with the Munich AI x biotech community. Thanks to Nucleate and Amino Collective for the invitation! See you there 🚀 luma.com/ehl0ap32

luma.com

Synapse Munich · Luma

Invite-only get-together with engineers, founders and scientists building at the intersection of AI, health & bio. Expect drinks, food, and some real talk…

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Fabian Theis @fabiantheis.bsky.social · 23/02/2026

🚀 From modality-specific to compositional foundation models for cell biology Happy to share our new Perspective in Cell Systems. We describe an emerging shift toward compositional multimodal architectures 🧩 authors.elsevier.com/c/1mdzg8YyDf...

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Fabian Theis @fabiantheis.bsky.social · 19/02/2026

Munich takes the top two spots in the FT ranking of Europe’s startup hubs — UnternehmerTUM #1, Start2 Group #2. Strong science, engineering depth, & real bridges between research + entrepreneurship. Huge opportunity ahead in part. for AI + bio/med. 🚀 www.ft.com/content/ab05...

ft.com

FT ranking: Europe’s leading start-up hubs 2026

View the top centres providing business incubator and accelerator programmes

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Fabian Theis @fabiantheis.bsky.social · 18/02/2026

Honored to receive today the official membership document of the @Leopoldina – Germany’s National Academy of Sciences – in Halle. “Nunquam otiosus” – never idle. A reminder that science is a continuous responsibility. And proud to be elected together with my AI & ELLIS colleague Sepp Hochreiter.

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Fabian Theis @fabiantheis.bsky.social · 14/02/2026

Where tech meets politics. At the #MSC Startup Hub, innovation & geopolitics collide in real time. Our @Helmholtz_de President Martin Keller is chairing session with former MI6, FBI/Interpol & Ukrainian security leader. Clearly security, crypto & AI are strategic capabilities.

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Fabian Theis @fabiantheis.bsky.social · 10/02/2026

🚀 New preprint: population-aware single-cell dynamics Collab w/ Bertie Göttgens’ lab, led by Weizhong. pseudodynamics+ goes beyond pseudotime to infer birth/death, differentiation & interpolate time in scalable fashion - directly from snapshot scRNA-seq. 👉 www.biorxiv.org/content/10.6...

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Fabian Theis @fabiantheis.bsky.social · 05/02/2026

CellRank protocol now in @NatureProtocols! 🎉 @PhilippWeiler's detailed guide shows how to: - Integrate velocity, pseudotime & time points - Infer cell fate probabilities - Analyze lineage priming at scale Great complement to our CellRank 2 paper! 📖 www.nature.com/articles/s41...

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Fabian Theis @fabiantheis.bsky.social · 04/02/2026

A recent @derspiegel article on “one of Germany’s most renowned AI researchers” got me thinking. The person was new to me, but I think highlights a somewhat recurring issue: media visibility is not the same as scientific contribution. www.spiegel.de/wissenschaft...

spiegel.de

(S+) Joscha Bach: Wie ein deutscher Forscher mit Epsteins Hilfe Karriere machte

Joscha Bach ist einer der renommiertesten deutschen KI-Forscher, offenbar hat er mehr als eine Million Dollar von Jeffrey Epstein erhalten. SPIEGEL-Recherchen zeigen: Der Kontakt reichte weit ins…

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Fabian Theis @fabiantheis.bsky.social · 03/02/2026

🚀 Interested in a postdoc in computational biology & AI for neuroscience? The NOMIS Synergy Fellowship offers a great opportunity to develop such a position in my lab within the interdisciplinary Synergy excellence cluster. 🔗 www.synergy-munich.de/news-events/...

synergy-munich.de

NOMIS–SyNergy Fellowship Program in Systems Neurology (Munich, Germany) | SyNergy - Munich Cluster for Systems Neurology

The NOMIS Foundation, in collaboration with the DFG-funded Munich Cluster for Systems Neurology (SyNergy), invites exceptional early-career scientists from around the world to apply for elite…

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Fabian Theis @fabiantheis.bsky.social · 03/02/2026

Congratulations to Matthias Tschöp on his inauguration as President of @LMU_Muenchen! A fitting moment to celebrate 200 years of LMU and to reflect on the responsibility and impact of universities & science in society.

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Fabian Theis @fabiantheis.bsky.social · 23/01/2026

🚀 Excited to share new paper in Nature Genetics: Human Retina Cell Atlas (HRCA) with ~4M cells, >130 retinal cell types, deep scRNA/ATAC integration. Enables cross-species comparisons & GWAS cell-type enrichment. Huge thanks to Ignacio Ibarra & Chen lab. www.nature.com/articles/s41...

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Fabian Theis @fabiantheis.bsky.social · 16/01/2026

Exciting Health AI session at #DLD2026 in Munich - with discussions about leveraging AI to integrate scales and design next experiments and treatments! A la DLD motto - it’s gonna get wild - follow at /www.dld-conference.com

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Fabian Theis @fabiantheis.bsky.social · 11/01/2026

A wonderful evening with my wife Michaela at the New Year’s Reception of the Bavarian Government ✨🥂

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Fabian Theis @fabiantheis.bsky.social · 08/01/2026

🔬 pertpy: a unified, scalable framework for single-cell perturbation analysis, now out in Nature Methods Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions. 👉 www.nature.com/articles/s41...

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Fabian Theis @fabiantheis.bsky.social · 08/01/2026

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Fabian Theis @fabiantheis.bsky.social · 19/12/2025

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."😅

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Fabian Theis @fabiantheis.bsky.social · 19/12/2025

🎄 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...

jobs.helmholtz-muenchen.de

Principal Investigators (f/m/x) for (i) AI in Biomedicine and (ii) AI Foundations

At Helmholtz Munich, we develop groundbreaking solutions for a healthier society in a rapidly changing world. We believe that diverse perspectives drive innovation. Through strong partnerships, we…

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Fabian Theis @fabiantheis.bsky.social · 15/12/2025

🚀 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...

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Fabian Theis @fabiantheis.bsky.social · 12/12/2025

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...

nature.com

Artificial intelligence agents for biology - Nature Methods

Artificial intelligence agents may have a transformative effect on how biological research is performed.

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Fabian Theis @fabiantheis.bsky.social · 10/12/2025

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...

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Fabian Theis @fabiantheis.bsky.social · 13/11/2025

🚀 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...

biorxiv.org

scConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction

Recent large-scale single-cell foundation models have shown promise for exploring cellular states, yet they often underperform compared to simpler, domain-specific methods, raising concerns about…

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Fabian Theis @fabiantheis.bsky.social · 07/11/2025

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

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Fabian Theis @fabiantheis.bsky.social · 04/11/2025

🚀 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

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Fabian Theis @fabiantheis.bsky.social · 03/11/2025

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. 🇪🇺

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Fabian Theis @fabiantheis.bsky.social · 03/11/2025

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 #AI #Munich #baiosphere

dealroom.co

The next generation of startup ecosystems: a benchmarking

This report is the conclusion of a data-driven analysis of 201 tech ecosystems. This set of actionable benchmarks is meant as a tool to help ecosystems understand and measure their maturity and…

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Fabian Theis @fabiantheis.bsky.social · 31/10/2025

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

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Fabian Theis @fabiantheis.bsky.social · 30/10/2025

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...

cruk.cam.ac.uk

Aliee Group - Cancer Research UK Cambridge Institute

Explain. Predict. Outsmart cancer.

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