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Fabian Theis
Helmholtz Munich | Matthias Tunger Photodesign

Prof. Dr. Dr. Fabian Theis

Director of the Computational Health Center, Director of the Institute for Computational Biology

"With AI we can imagine a future where diagnosing and treating diseases is more affordable, widely available, and thus more democratic."

"With KI we can imagine a future where diagnosing and treating diseases is more affordable, widely available, and thus more democratic."

Academic career and research areas

Fabian Theis uses artificial intelligence to uncover the secrets of human cells. How do they interact and what's going wrong at the cellular level when someone falls ill? By using single-cell sequencing data and machine learning, he and his team are able to model cellular variety and make predictions in biology and biomedicine.

Fabian holds two Master's Degrees in Mathematics and Physics, as well as two Doctorates in Physics and Computer Science.

Fabian’s career began as head of the research group “Signal Processing and Information Theory” at the Institute for Biophysics in Regensburg. As a Bernstein Fellow, he led a junior researcher group at the Bernstein Center for Computational Neuroscience at the Max Planck Institute for Dynamics and Self-Organization in Göttingen in 2006. One year later he became head of a task force at the Institute for Bioinformatics at Helmholtz Munich. After two years he was then appointed Extracurricular Professor for Mathematics in System Biology at the Technical University of Munich.

Fabian has served as a guest scientist at various international institutes, such as the Department of Architecture and Computer Technology of the University of Granada, Spain; the RIKEN Brain Science Institute in Wako, Japan; FAMU/FSU in Florida, USA; and TUAT’s Laboratory for Signal and Image Processing in Tokyo, Japan.

Fabian now leads the Computational Health Center at Helmholtz Munich, where seven institutes are researching the relationship between artificial intelligence and health. He also chairs the Mathematical Modeling of Biological Systems program at the Technical University of Munich. As Science Director at HelmholtzAI, Fabian Theis coordinates various initiatives and networks, including:

  • Analysis Working Group of the Human Cell Atlas
  • Single Cell Omics Germany (SCOG)
  • Munich School for Data Science (MUDS)
  • ELLIS Munich

Focus areas, skills, expertise

Artificial intelligence  Big DataDeep learning Machine learningSingle-cell analysisBiostatisticsCell mappingDynamic systemsStochastic modeling


Honors and Awards

Gottfried Wilhelm Leibniz-Preis
ERC Advanced Grant
Hamburger Wissenschaftspreis
Erwin Schrödinger Preis
ERC Starting Grant

What does Big Data do for medicine?

Fabian Theis on Schwanke meets Science

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Sikkema, L., Ramírez-Suástegui, C., Strobl, D. C., Gillett, T. E., Zappia, L., Madissoon, E., Markov, N. S., Zaragosi, L.-E., Ji, Y., Ansari, M., Arguel, M.-J., Apperloo, L., Banchero, M., Bécavin, C., Berg, M., Chichelnitskiy, E., Chung, M.-I., Collin, A., Gay, A. C. A.,Theis, F. J. 2023. An integrated cell atlas of the lung in health and disease. Nature Medicine, 29(6), 1563–1577Nature Medicine.

Fischer, D.S., Schaar, A.C. & Theis, F.J. 2022. Modeling intercellular communication in tissues using spatial graphs of cells. Nature Biotechnology.

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.2022. Squidpy: A Scalable Framework for Spatial Single Cell Analysis. Nature Methods.

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. 2022. CellRank for directed single-cell fate mapping. Nature Methods.

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. 2022. Benchmarking atlas-level data integration in single-cell genomics. Nature Methods.