Fabian Theis
@fabiantheis.bsky.social
Computational biologist @HelmholtzMunich, prof @TU_Muenchen & associate PI @sangerinstitute. Dad of 4 and mountain lover. Department news, see @CompHealthMuc
๐ New preprint: population-aware single-cell dynamics
Collab w/ Bertie Gรถttgensโ lab, led by Weizhong.
pseudodynamics+ goes beyond pseudotime to infer birth/death, differentiation & interpolate time in scalable fashion - directly from snapshot scRNA-seq.
๐ www.biorxiv.org/content/10.6...
Collab w/ Bertie Gรถttgensโ lab, led by Weizhong.
pseudodynamics+ goes beyond pseudotime to infer birth/death, differentiation & interpolate time in scalable fashion - directly from snapshot scRNA-seq.
๐ www.biorxiv.org/content/10.6...
February 10, 2026 at 1:40 PM
๐ New preprint: population-aware single-cell dynamics
Collab w/ Bertie Gรถttgensโ lab, led by Weizhong.
pseudodynamics+ goes beyond pseudotime to infer birth/death, differentiation & interpolate time in scalable fashion - directly from snapshot scRNA-seq.
๐ www.biorxiv.org/content/10.6...
Collab w/ Bertie Gรถttgensโ lab, led by Weizhong.
pseudodynamics+ goes beyond pseudotime to infer birth/death, differentiation & interpolate time in scalable fashion - directly from snapshot scRNA-seq.
๐ www.biorxiv.org/content/10.6...
CellRank protocol now in @NatureProtocols! ๐
@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!
๐ www.nature.com/articles/s41...
@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!
๐ www.nature.com/articles/s41...
February 5, 2026 at 7:37 PM
CellRank protocol now in @NatureProtocols! ๐
@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!
๐ www.nature.com/articles/s41...
@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!
๐ www.nature.com/articles/s41...
Reposted by Fabian Theis
Did you catch our recent Protocol describing the inference of cell fate from single-cell RNA sequencing data using CellRank?
๐งช @natprot.nature.com @fabiantheis.bsky.social
๐งช @natprot.nature.com @fabiantheis.bsky.social
CellRank: consistent and data view agnostic fate mapping for single-cell genomics - Nature Protocols
CellRank enables cell fate mapping from single-cell RNA sequencing data in a consistent and scalable manner, relying on different views of the data such as pseudotime or stemness potential, RNA veloci...
www.nature.com
February 4, 2026 at 6:12 AM
Did you catch our recent Protocol describing the inference of cell fate from single-cell RNA sequencing data using CellRank?
๐งช @natprot.nature.com @fabiantheis.bsky.social
๐งช @natprot.nature.com @fabiantheis.bsky.social
A recent @derspiegel article on โone of Germanyโs most renowned AI researchersโ 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...
www.spiegel.de/wissenschaft...
(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 insโฆ
www.spiegel.de
February 4, 2026 at 1:32 PM
A recent @derspiegel article on โone of Germanyโs most renowned AI researchersโ 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...
www.spiegel.de/wissenschaft...
๐ 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.
๐ www.synergy-munich.de/news-events/...
The NOMIS Synergy Fellowship offers a great opportunity to develop such a position in my lab within the interdisciplinary Synergy excellence cluster.
๐ www.synergy-munich.de/news-events/...
NOMISโSyNergy 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 eliteโฆ
www.synergy-munich.de
February 3, 2026 at 5:52 PM
๐ 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.
๐ www.synergy-munich.de/news-events/...
The NOMIS Synergy Fellowship offers a great opportunity to develop such a position in my lab within the interdisciplinary Synergy excellence cluster.
๐ www.synergy-munich.de/news-events/...
Congratulations to Matthias Tschรถp 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.
February 3, 2026 at 5:26 PM
Congratulations to Matthias Tschรถp 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.
๐ 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...
www.nature.com/articles/s41...
January 23, 2026 at 2:22 PM
๐ 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...
www.nature.com/articles/s41...
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 - itโs gonna get wild - follow at /www.dld-conference.com
January 16, 2026 at 9:20 AM
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 - itโs gonna get wild - follow at /www.dld-conference.com
A wonderful evening with my wife Michaela at the New Yearโs Reception of the Bavarian Government โจ๐ฅ
January 11, 2026 at 4:33 PM
A wonderful evening with my wife Michaela at the New Yearโs Reception of the Bavarian Government โจ๐ฅ
๐ฌ 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.
๐ www.nature.com/articles/s41...
Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions.
๐ www.nature.com/articles/s41...
January 8, 2026 at 4:30 PM
๐ฌ 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.
๐ www.nature.com/articles/s41...
Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions.
๐ www.nature.com/articles/s41...
๐ฌ 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.
๐ www.nature.com/articles/s41...
Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions.
๐ www.nature.com/articles/s41...
January 8, 2026 at 4:30 PM
๐ฌ 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.
๐ www.nature.com/articles/s41...
Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions.
๐ www.nature.com/articles/s41...
Thanks to team for wonderful lab xmas party yesterday! ๐๐
๐ผ Besides Feuerzangenbowle (=mulled wine^2) we had this funny guess-the-paper from Santa's crazy review. Not sure you can guess the paper ๐, but I loved ~summary "Benchmarking the benchmark of benchmarking benchmarks."๐
December 19, 2025 at 7:28 PM
Thanks to team for wonderful lab xmas party yesterday! ๐๐
๐ผ Besides Feuerzangenbowle (=mulled wine^2) we had this funny guess-the-paper from Santa's crazy review. Not sure you can guess the paper ๐, but I loved ~summary "Benchmarking the benchmark of benchmarking benchmarks."๐
๐ Weโre hiring in Health AI at @HelmholtzMunich!
๐น PIs in Health AI/AI Foundations
๐น Health AI Fellows
๐น Clinical AI Consultants
Apply๐
PIs: jobs.helmholtz-muenchen.de/jobposting/8...
Fellows: jobs.helmholtz-muenchen.de/jobposting/7...
Consult: jobs.helmholtz-muenchen.de/jobposting/c...
๐น PIs in Health AI/AI Foundations
๐น Health AI Fellows
๐น Clinical AI Consultants
Apply๐
PIs: jobs.helmholtz-muenchen.de/jobposting/8...
Fellows: jobs.helmholtz-muenchen.de/jobposting/7...
Consult: jobs.helmholtz-muenchen.de/jobposting/c...
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, weโฆ
jobs.helmholtz-muenchen.de
December 19, 2025 at 3:49 PM
๐ Weโre hiring in Health AI at @HelmholtzMunich!
๐น PIs in Health AI/AI Foundations
๐น Health AI Fellows
๐น Clinical AI Consultants
Apply๐
PIs: jobs.helmholtz-muenchen.de/jobposting/8...
Fellows: jobs.helmholtz-muenchen.de/jobposting/7...
Consult: jobs.helmholtz-muenchen.de/jobposting/c...
๐น PIs in Health AI/AI Foundations
๐น Health AI Fellows
๐น Clinical AI Consultants
Apply๐
PIs: jobs.helmholtz-muenchen.de/jobposting/8...
Fellows: jobs.helmholtz-muenchen.de/jobposting/7...
Consult: jobs.helmholtz-muenchen.de/jobposting/c...
๐ 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, Sรถren, Larsen, Parse Bio & Seelig lab!
๐ www.biorxiv.org/content/10.6...
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, Sรถren, Larsen, Parse Bio & Seelig lab!
๐ www.biorxiv.org/content/10.6...
December 15, 2025 at 10:42 PM
๐ 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, Sรถren, Larsen, Parse Bio & Seelig lab!
๐ www.biorxiv.org/content/10.6...
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, Sรถren, Larsen, Parse Bio & Seelig lab!
๐ www.biorxiv.org/content/10.6...
Nature Methods names AI agents a โMethod to Watchโ!
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...
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...
Artificial intelligence agents for biology - Nature Methods
Artificial intelligence agents may have a transformative effect on how biological research is performed.
www.nature.com
December 12, 2025 at 3:46 PM
Nature Methods names AI agents a โMethod to Watchโ!
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...
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 โunassigned RNAsโ in imaging-based spatial transcriptomics. Across technologies, 30-40% of transcripts fall outside segmentation, & many show structured, biologically meaningful extrasomatic patterns.
๐ www.biorxiv.org/content/10.6...
๐ www.biorxiv.org/content/10.6...
December 10, 2025 at 3:21 PM
Excited to share new preprint led by Sergio Salas on โunassigned RNAsโ in imaging-based spatial transcriptomics. Across technologies, 30-40% of transcripts fall outside segmentation, & many show structured, biologically meaningful extrasomatic patterns.
๐ www.biorxiv.org/content/10.6...
๐ www.biorxiv.org/content/10.6...
๐ 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.
๐ www.biorxiv.org/content/10.1...
We move beyond reconstruction to learn rich, cell-level embeddings for diverse omics.
๐ 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 aboutโฆ
www.biorxiv.org
November 13, 2025 at 5:17 PM
๐ 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.
๐ www.biorxiv.org/content/10.1...
We move beyond reconstruction to learn rich, cell-level embeddings for diverse omics.
๐ 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
๐ 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 ๐งฌ๐
๐ 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 ๐งฌ๐
๐ biorxiv.org/content/10.1...
#AI #Biology #DeepLearning
November 4, 2025 at 5:40 PM
๐ 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 ๐งฌ๐
๐ 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 ๐งฌ๐
๐ biorxiv.org/content/10.1...
#AI #Biology #DeepLearning
EU commissioner Henna Virkkunen officially launching EUโs 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. ๐ช๐บ
November 3, 2025 at 2:26 PM
EU commissioner Henna Virkkunen officially launching EUโs 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. ๐ช๐บ
Munich is now the #2 AI ecosystem in Europe (after Paris) and #11 globally, per Dealroomโs Global Tech Ecosystem Index 2025! ๐ฉ๐ช๐ค๐ซ๐ท
Proud of the growing strength of the Bavarian AI ecosystem ๐ baiosphere.org๏ฟผ
๏ฟฝ๏ฟฝ dealroom.co/tech-ecosystem-index-2025๏ฟฝ5#Munich #baiosphereiosphere
Proud of the growing strength of the Bavarian AI ecosystem ๐ baiosphere.org๏ฟผ
๏ฟฝ๏ฟฝ dealroom.co/tech-ecosystem-index-2025๏ฟฝ5#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 andโฆ
dealroom.co
November 3, 2025 at 9:00 AM
Munich is now the #2 AI ecosystem in Europe (after Paris) and #11 globally, per Dealroomโs Global Tech Ecosystem Index 2025! ๐ฉ๐ช๐ค๐ซ๐ท
Proud of the growing strength of the Bavarian AI ecosystem ๐ baiosphere.org๏ฟผ
๏ฟฝ๏ฟฝ dealroom.co/tech-ecosystem-index-2025๏ฟฝ5#Munich #baiosphereiosphere
Proud of the growing strength of the Bavarian AI ecosystem ๐ baiosphere.org๏ฟผ
๏ฟฝ๏ฟฝ dealroom.co/tech-ecosystem-index-2025๏ฟฝ5#Munich #baiosphereiosphere
Reposted by Fabian Theis
๐ 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
๐ To the original publication in Nature Methods: t1p.de/ba2gx
@fabiantheis.bsky.social @comphealthmunich.bsky.social
@fabiantheis.bsky.social @comphealthmunich.bsky.social
๐ Happy Halloween from our Lab! ๐ป๐งฌ
No bad computational tricks โ only treats! ๐งซ๐ปโจ
No bad computational tricks โ only treats! ๐งซ๐ปโจ
October 31, 2025 at 11:18 AM
๐ Happy Halloween from our Lab! ๐ป๐งฌ
No bad computational tricks โ only treats! ๐งซ๐ปโจ
No bad computational tricks โ only treats! ๐งซ๐ปโจ
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...
๐งฌ 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 ๐
๐ 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 ๐
๐ www.nature.com/articles/s41...
October 30, 2025 at 7:19 PM
๐งฌ 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 ๐
๐ 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 ๐
๐ www.nature.com/articles/s41...