Prof. Dr. Dr. Fabian Joachim Theis

Technische Universität München, Fakultät Mathematik

Boltzmannstr. 3
85748 Garching
Phone: +49 89 3187-2211

University training and degree

10/2001 – 12/2003 Doctoral Degree in Computer Science, Prof. C. Puntonet, University of Granada; ‘Geometric Source Separation’, grade `sobresaliente cum laude’ (highest)
01/2001 – 12/2002 degree in Physics, Prof. E. Lang, Biophysics, University of Regensburg; ‘Mathematics in Independent Component Analysis’, grade `summa cum laude’ (highest)
10/1996 -12/2000 Study in Physics, University of Regensburg
Diploma in Physics, grade ‘1.0 mit Auszeichnung’ (highest, with distinction)
10/1995 – 03/2000 Study in Mathematics, University of Regensburg
Diploma in Mathematics, grade ‘sehr gut’ (highest)

Advanced academic qualifications

06/2008 Habilitation in Biophysics, University of Regensburg

Postgraduate professional career

Since 06/2019 Associate Faculty, Wellcome Trust Sanger Institute, Hinxton, UK
Since 04/2019 Scientific director Helmholtz Artificial Intelligence Cooperation Unit (Helmholtz AI), Helmholtz Zentrum München, Germany
Since 06/2013 Director of the Institute of Computational Biology (ICB), Helmholtz Zentrum München, Germany
Since 06/2013 Full Professor (chair, W3) ‘Mathematical Modeling of Biological Systems’ Department of Mathematics, Technical University Munich, Germany
Since 10/2013 Adjunct Professor at the Department of Life Sciences, Technical University Munich, Germany
03/2009 – 05/2013 Associate Professor (W2) for ‘Mathematics in Systems Biology’, at the Department of Mathematics, Technical University Munich, Germany
07/2007 – 05/2013 Junior group leader ‘Computational Modeling in Biology’ at the Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Germany
09/2006 – 07/2007 Independent researcher (Bernstein fellow) at the Bernstein Center for Computational Neuroscience Göttingen & Max-Planck-Institute for Dynamics and Self- Organization, Göttingen, Germany, Prof. T. Geisel
03/2005 – 10/2005 visiting researcher TUAT, Tokyo, Japan, Prof. T. Tanaka, JSPS fellow
08/2004 visiting researcher HUT, Helsinki, Finland, Prof. J. Karhunen and Prof. E. Oja
02/2004 – 03/2004 visiting researcher at FSU, Tallahassee, Prof. A. Meyer-Bäse
10/2003 – 11/2003 visiting researcher at RIKEN, Tokyo, Prof. A. Cichocki
03/2003 – 08/2006 Postdoctoral fellow Biophysics, University of Regensburg, Prof. E. Lang, DFG-graduate College ‘Nonlinearity&Nonequilibrium in Condensed Matter’’
Since 09/2000 Company ‘Instant Solutions Ltd.’, co-funded with J. Müller, web-based database applications, 5 employees

Since 2020 Member of the Scientific Advisory Board of the Berlin Institute of Health
Since 2020 Co-Coordinator of the ELLIS unit Munich
Since 2019 Member of EMBL’s Scientific Advisory Committee
Since 2019 Member of the Steering Committee of the Human Cell Atlas Lung Seed Network
Since 2019 Coordinator  Helmholtz Artificial Intelligence Cooperation Unit (Helmholtz AI)
Since 2019 Member of the Management Committee of the Helmholtz Zentrum München
Since 2018 Coordinator of the Munich School for Data Science (MUDS)
Since 2018 Appointment as expert of the German ‘Wissenschaftsrat’ (Science Council)
Since 2018 Coordinator and member of the ‘Single Cell Omics network Germany’
Since 2017 Member of the Computational Steering Committee and Data Pipeline Committee of the Human Cell Atlas Initiative
2017 Erwin Schrödinger Award, Stifterverband, Helmholtz Association
2015 M4 award, Bavarian Biotechnological Cluster
2015 Almirall Förderpreis and Oscar-Gans Award
Since 2014 Jury member for ‘Nachwuchspreis’ of ‘academics’
Since 2014 Member of the ‘International Society of Computational Biology’ (ISCB)
2010 ERC Starting Grant ‘Modelling Latent Causes in Molecular Networks’
2009 – 2014 Member of the ‘Young Academy’
2006 ‘Heinz Maier-Leibnitz Award’ (DFG)

a) Articles published by outlets with scientific quality assurance, book publications and works accepted for publication, but not yet published

1. Bergen, V, Lange, M, Peidli, S, Wolf FA°, Theis, FJ°. Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology (2020) doi:10.1038/s41587-020-0591-3

2. 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)

3. 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)

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

5. 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)

6. 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)

7. 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)

8. 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)

9. 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)

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