Fabian Theis
@fabiantheis.bsky.social
Computational biologist @HelmholtzMunich, prof @TU_Muenchen & associate PI @sangerinstitute. Dad of 4 and mountain lover. Department news, see @CompHealthMuc
🚀 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...
We move beyond reconstruction to learn rich, cell-level embeddings for diverse omics.
📘 www.biorxiv.org/content/10.1...
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…
www.biorxiv.org
November 13, 2025 at 5:17 PM
🚀 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...
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
Our goal: virtual twin cells, tissues & patients.
#AIinMedicine #HelmholtzMunich
November 7, 2025 at 6:55 PM
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
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
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
November 4, 2025 at 5:40 PM
🚀 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
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. 🇪🇺
November 3, 2025 at 2:26 PM
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
Proud of the growing strength of the Bavarian AI ecosystem 👉 baiosphere.org
�� dealroom.co/tech-ecosystem-index-2025�5#Munich #baiosphereiosphere
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…
dealroom.co
November 3, 2025 at 9:00 AM
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
Proud of the growing strength of the Bavarian AI ecosystem 👉 baiosphere.org
�� dealroom.co/tech-ecosystem-index-2025�5#Munich #baiosphereiosphere
Reposted by Fabian Theis
🔗 To the original publication in Nature Methods: t1p.de/ba2gx
@fabiantheis.bsky.social @comphealthmunich.bsky.social
@fabiantheis.bsky.social @comphealthmunich.bsky.social
Nicheformer: a foundation model for single-cell and spatial omics - Nature Methods
Pretrained on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances toward building foun...
t1p.de
October 30, 2025 at 10:09 AM
🔗 To the original publication in Nature Methods: t1p.de/ba2gx
@fabiantheis.bsky.social @comphealthmunich.bsky.social
@fabiantheis.bsky.social @comphealthmunich.bsky.social
🎃 Happy Halloween from our Lab! 👻🧬
No bad computational tricks — only treats! 🧫💻✨
No bad computational tricks — only treats! 🧫💻✨
October 31, 2025 at 11:18 AM
🎃 Happy Halloween from our Lab! 👻🧬
No bad computational tricks — only treats! 🧫💻✨
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...
Aliee Group - Cancer Research UK Cambridge Institute
Explain. Predict. Outsmart cancer.
www.cruk.cam.ac.uk
October 30, 2025 at 8:38 PM
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...
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...
October 30, 2025 at 7:19 PM
🧬 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...
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
October 30, 2025 at 12:50 PM
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
Reposted by Fabian Theis
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...
doi.org/10.1101/2025...
scPortrait integrates single-cell images into multimodal modeling
Machine learning increasingly uncovers rules of biology directly from data, enabled by large, standardized datasets. Microscopy images provide rich information on cellular architecture and are accessi...
doi.org
September 24, 2025 at 12:22 PM
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...
doi.org/10.1101/2025...
Reposted by Fabian Theis
✨ 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
👉Read more: t1p.de/5wthc
#AIinMedicine #DigitalHuman #PrecisionMedicine
October 28, 2025 at 6:43 AM
✨ 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
👉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
October 28, 2025 at 9:14 AM
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
@eriktopol
October 27, 2025 at 5:43 PM
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
@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.
Excited for the Bavarian AI in Medicine Conference tomorrow.
October 26, 2025 at 9:29 PM
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.
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. 💡
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. 💡
Bavarian Conference on AI in Medicine
We are excited to invite you to the Bavarian Conference on AI in Medicine where we will explore the intersection of artificial intelligence and medical research. This event is aimed at Bavarian PhD st...
events.hifis.net
October 25, 2025 at 2:50 PM
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. 💡
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. 🔁
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. 🔁
October 25, 2025 at 1:24 PM
🚀 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. 🔁
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!
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!
October 9, 2025 at 8:56 PM
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!
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...
🔗 www.biorxiv.org/content/10.1...
September 28, 2025 at 5:50 PM
🚀 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...
🔗 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
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
The research and innovation community platform
The research and innovation community platform is a unique space bringing together researchers from the EU and beyond. Take part in events, access exclusive content, and widen your network.
research-innovation-community.ec.europa.eu
September 17, 2025 at 7:04 AM
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
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
¡¡El Flashmob Bohemian Rhapsody más INCREÍBLE que jamás verás!!😍
youtu.be
September 11, 2025 at 8:00 AM
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
🚀https://dld-conference.com
September 10, 2025 at 8:30 AM
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
🚀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/...
📄 www.science.org/doi/10.1126/...
September 8, 2025 at 3:23 PM
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/...
📄 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!
September 3, 2025 at 10:40 AM
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!
Reposted by Fabian Theis
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
Many thanks to all involved, especially Blueskyless Nil Uresin and Sabrina Richer and my co-PIs @fabiantheis.bsky.social and @erwinschoof.bsky.social
We’re excited to present this integrative analysis of single-cell proteomics and transcriptomics of the human HSPC hierarchy. Now published in @science.org together with @fabiantheis.bsky.social, @erwinschoof.bsky.social, @porsebo.bsky.social.
www.science.org/doi/10.1126/...
🧵
www.science.org/doi/10.1126/...
🧵
Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics
Single-cell transcriptomics (scRNA-seq) has facilitated the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, the exclusive use of mRNA measurem...
www.science.org
August 22, 2025 at 10:51 AM
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
Many thanks to all involved, especially Blueskyless Nil Uresin and Sabrina Richer and my co-PIs @fabiantheis.bsky.social and @erwinschoof.bsky.social