Source: HMGU

Prof. Dr. Dr. Fabian Theis
Institute Director and Research Group Leader

Phone: +49 89 3187-43260
Building/Room: 58a / 112


Fabian Theis uses artificial intelligence to unlock the secrets of human cells. How do they interact and what goes wrong with diseases at the cellular level? Single cell sequencing allows him and his team to analyse and model single cell heterogeneities, as well as using machine and deep learning for prediction in biology and biomedicine.

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Fabian Theis is head of the Computational Health Center at Helmholtz Munich and holds the chair "Mathematical Modeling of Biological Systems" at the Department of Mathematics of the Technical University of Munich. He is director of HelmholtzAI and Associate Faculty at the Wellcome Trust Sanger Institute since 2019 as well as member and/or coordinator of various initiatives:

Fabian holds MSc degrees in Mathematics and Physics (University of Regensburg, 2000) a PhD degree in Physics from the same university (2002) and a PhD in Computer Science (University of Granada, 2003). In 2017, he was awarded the Erwin Schrödinger prize together within an interdisciplinary team at the ETH Zürich.

He has been working as visiting researcher at the department of Architecture and Computer Technology (University of Granada, Spain), at the RIKEN Brain Science Institute (Wako, Japan), at FAMU-FSU (Florida State University, USA) and at TUAT's Laboratory for Signal and Image Processing (Tokyo, Japan).

As a principal researcher, he led the 'Signal processing & information theory' group at the Institute of Biophysics in Regensburg, Germany. In 2006, he headed a junior research group as Bernstein fellow at the Bernstein Center for Computational Neuroscience, within the Max Planck Institute for Dynamics and Self-Organisation in Göttingen. 2007, he became working group head of CMB at the Institute of Bioinformatics at Helmholtz Munich. Two years later, he became Associate Professor for Mathematics in Systems Biology at TU Munich. From 2009 to 2014 he was also member of the ‘Young Academy’ (founded by the Berlin-Brandenburg Academy of Sciences and Humanities and the German Academy of Natural Scientists Leopoldina) and in 2010 he was awarded an ERC starting grant.  In 2021 he was awarded the Hamburg Science price - the highest endowed price by a german science academy.


Selected Publications

Palla, G., Spitzer, H., Klein, M., Fischer, D., Schaar, A.C., Kuemmerle, L.B., Rybakov, S., Ibarra, I.L., Holmberg, O., Virshup, I., Lotfollahi, M., Richter, S., Theis, F.J. Squidpy: A Scalable Framework for Spatial Single Cell Analysis. Nat. Methods (2022, in press)

Lange, M., Bergen, V., Klein, M., Setty, M., Reuter, B., Bakhti, M, Lickert, H. Ansari, M. Schniering, J. Schuller, H.B., Peér D.°, Theis F.J.° CellRank for directed single-cell fate mapping. Nat. Methods (2022)

Luecken, M.D, Büttner, M. Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., Theis, F.J. Benchmarking atlas-level data integration in single-cell genomics. Nat. Methods 19, 41–50 (2022)

Böttcher, A., Büttner, M., Tritschler, S., Sterr, M., Aliluev, A., Oppenländer, L., Burtscher, I., Sass, S., Irmler, M., Beckers, J., Ziegenhain, C., Enard, W., Schamberger, A.C., Verhamme, F.M., Eickelberg, O., Theis, F.J.°, Lickert, H.° Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates. Nat. Cell Biol. 23, 23-31 (2021) 

Büttner, M., Ostner, J., Müller, C., Theis, F.J., Schubert, B. scCODA is a Bayesian model for compositional single-cell data analysis. Nat. Commun. 12:6876 (2021)

Lotfollahi, M., Naghipourfar, M., Luecken, M., Khajavi, M., Büttner, M., Wagenstetter, M., Avsec, Z., Gayoso, A., Yosef, N., Interlandi, M., Rybakov, S., Misharin, A.V., Theis, F.J. Mapping single-cell data to reference atlases by transfer learning. Nat. Biotechnol., DOI: 10.1038/s41587-021-01001-7 (2021)

Bergen, V., Lange, M., Peidli, S., Wolf F.A., Theis,F.J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology. doi:10.1038/s41587-020-0591-3 (2020). For press release click here

Böttcher, A, Büttner, M, Tritschler, S, [...], Theis, FJ°, Lickert, H°. Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells. accepted at Nature Cell Biology (2020)

Sachs S, Bastidas-Ponce, A, Tritschler, S, [...]., Tschöp, MH, Theis, FJ°, Hofmann, SM°, Müller, TD°, Lickert, H°. Targeted pharmacological therapy restores β-cell function for diabetes remission. Nature Metabolism 2, 192–209 (2020). For press release click here

Lotfollahi, M, Wolf, FA and Theis, FJ. scGen predicts single-cell perturbation responses. Nature Methods 16, 715–721 (2019). For press release click here

Fischer, DS, Fiedler, AK, Kernfeld, E, Genga, RM, Hasenauer, J, Maehr, R., Theis, FJ. Inferring population dynamics from single-cell RNA-sequencing time series data. Nature Biotechnology 37, 461–468 (2019). For press release click here

Buettner, M, Miao, Z, Wolf, FA, Teichmann, SA°, Theis, FJ°. A test metric for assessing single-cell RNA-seq batch correction. Nature Methods 19, 43–49 (2019)

Eraslan, G, Simon, L, Mircea, M, Mueller, NS, Theis, FJ. Single cell RNA-seq denoising using a deep count autoencoder. Nature Communications 10, 390 (2019)

 Wolf, F, Angerer, P, Theis, FJ. SCANPY: Large-scale single-cell gene expression data analysis. Genome Biology 19, 15 (2019). (ranked most cited paper that year from Gen Biol). For press release click here

Buggenthin, F, Buettner, F, Hoppe, PS, Endele, M, Kroiss, M, Strasser, M, Schwarzfischer, M, Loeffler, D, Kokkaliaris, KD, Hilsenbeck, O, Schroeder, T°, Theis, FJ°, Marr, C°. Prospective identification of hematopoietic lineage choice by deep learning. Nature Methods 14 403–406 (2017). For press release click here

Haghverdi, L, Buettner, M,  Wolf FA , Buettner F, Theis FJ. Diffusion pseudotime robustly reconstructs lineage branching. Nature Methods 13, 845–848 (2016). For press release click here

 ° joint corresponding authors


Selected News (since 2019)

12.11.2020 "I can see it in your eyes”: Novel deep learning method enables clinic-ready automated screening for diabetes-related eye disease

11.11.2020 A strong ecosystem for the “AI of the future” on a European Level

06.11.2020 Fabian Theis: The data juggler

15.09.2020 Munich joins the ELLIS unit network to help shape the future of AI in Europe

03.08.2020 AI & single-cell genomics: New software predicts cell fate

17.06.2020 Helmholtz funds 19 AI projects to solve urgent grand challenges

11.05.2020 Coronavirus research combines forces: Genome researchers create German COVID-19 OMICS Initiative (DeCOI)

16.04.2020 Why smokers, men, and older people tend to be more severely affected by COVID-19?

20.02.2020 New drug combination restores beta cell function in animal model: potential for diabetes remission

01.12.2019 EU supports excellence in research at Helmholtz Zentrum München with more than 8 million Euros funding

26.03.2019 Helmholtz: New AI flagship unit in Munich to strengthen its Germany-wide research network