back to staff

Profile Prof. Dr. Olaf Wolkenhauer

Head of Section III (ad interim) &
Unit Head Network Modeling & Machine Learning

Lise-Meitner-Str. 34
85354 Freising
Germany
Tel.: +49 1717410731

Email  ORCID

I am a data scientist, using mathematics and computational tools to make sense of data. My work focusses on understanding how the functioning of cellular systems emerges from the interactions between the system’s parts, and how these emergent properties of a system as a whole enable or constrain the behaviour of its parts. Despite technological advances, that allow us to identify and characterise cellular components, the principles by which cells and tissues realise their function, remain poorly understood. My approach combines data-driven modelling with model-driven experimentation, using a wide range of computational and mathematical tools, including machine learning, statistics, systems theory, and stochastic processes. The results of my work support basic biological and medical research.

Since 2020 Guest Professor, Interim Head of Section III, Leibniz Institute for Food Systems Biology, at TU Munich.
Since 2018 Adj. Professor, Chhattisgarh Swami Vivekanand Technical University, India
Since 2005 Adj. Professor in the Dept. of Electrical Engineering & Computer Science Case Western Reserve University, Cleveland, Ohio, USA
Since July 2003 Full Professor (W3/C4), Chair in Systems Biology & Bioinformatics, Faculty of Computer Science & Electrical Engineering, University of Rostock
2002 – 2003 Senior Lecturer. Joint appointment between the Dept. of Biomolecular Sciences and the Dept. of Electrical Engineering & Electronics. UMIST (University of Manchester, Institute of Science & Technology), Manchester, UK
2000 – 2002 Lecturer. Joint appointment between the Control Systems Centre and the Department of Biomolecular Sciences, UMIST, Manchester, UK
1999 – 2000 Senior Research Fellow (by invitation). Faculty of Information Technology and Systems, Delft University of Technology, Netherlands
1997 – 2000 Lecturer, Lucas Varity Research Lectureship, Control Systems Centre, UMIST, Manchester, UK
1994 – 1997 Research Associate at the Control Systems Centre, UMIST, Manchester, UK. Ph.D. Thesis title: “Possibility Theory with Applications to Data Analysis”
  • SPIE Pioneer Award (2009)
  • IBM Computing Prize (1994)

My expertise is in data analysis and mathematical modelling, focusing on applications to the life sciences. My work covers a range of interdisciplinary interactions: (i) I support biomedical researchers with workflows to analyse their wet-lab data. (ii) I work with pharma companies to explain how their products modulate molecular and cellular networks. (iii) IT companies fund us to develop for them machine learning workflows and algorithms to detect pattern in data. (iv) Supporting clinicians with the use of machine and deep learning approaches in clinical decision making. A list of projects can be found at www.sbi.uni-rostock.de

  • BioSystems Modelling and Simulation (Summer semester). 4 SWS
  • Modelling and Simulation with Application to the Life Sciences (Winter semester)
  • Data Science with Python. 2 SWS (Summer and Winter Semester)

(See ORCID for complete list)

1.         Apweiler, R., Beissbarth, T., Berthold, M.R., Blüthgen, N., Burmeister, Y., Dammann, O., Deutsch, A., Feuerhake, F., Franke, A., …, Wolkenhauer, O., 2018. Whither systems medicine? Exp. Mol. Med. doi.org/10.1038/emm.2017.290

2.         Bej, S., Davtyan, N., Wolfien, M., Nassar, M., Wolkenhauer, O., 2020. LoRAS: An oversampling approach for imbalanced datasets. Mach. Learn. DOI: 10.1007/s10994-020-05913-4

3.         Dreyer, F.S., Cantone, M., …, Gupta, S.K., Khan, F.M., Wolkenhauer, O., Pützer, B.M., Jäck, H.M., Heinzerling, L., Vera, J., 2018. A web platform for the network analysis of high-throughput data in melanoma and its use to investigate mechanisms of resistance to anti-PD1 immunotherapy. Biochim. Biophys. Acta - Mol. Basis Dis. doi.org/10.1016/j.bbadis.2018.01.020

4.         Goody, D., Gupta, S.K., Engelmann, D., …, Wolkenhauer, O., Logotheti, S., Pützer, B.M., 2019. Drug repositioning inferred from E2F1-coregulator interactions studies for the prevention and treatment of metastatic cancers. Theranostics. doi.org/10.7150/thno.29546

5.         Wang, Y., Alla, V., Goody, D., Gupta, S.K., Spitschak, A., Wolkenhauer, O., Pützer, B.M., Engelmann, D., 2016. Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signatures. Nucleic Acids Res. 44. doi.org/10.1093/nar/gkv885

6.         Khan, F.M., Marquardt, S., Gupta, S.K., Knoll, S., Schmitz, U., Spitschak, A., Engelmann, D., Vera, J., Wolkenhauer, O., Pützer, B.M., 2017. Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. Nat. Commun. 8, 198. doi.org/10.1038/s41467-017-00268-2

7.         Lai, X., Gupta, S.K., Schmitz, U., ..., Wolkenhauer, O., Pützer, B.M., Vera, J., 2018. MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics 8. doi.org/10.7150/thno.19904

8.         Ostaszewski, M., Mazein, A., Gillespie, M.E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A.R., …, Wolkenhauer, O., Furlong, L.I., …, Schneider, R., 2020. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci. Data. doi.org/10.1038/s41597-020-0477-8

9.         Serhan, C.N., Gupta, S.K., Perretti, M., Godson, C., Brennan, E., Li, Y., Soehnlein, O., Shimizu, T., Werz, O., Chiurchiù, V., Azzi, A., Dubourdeau, M., ..., Wolkenhauer, O., 2020. The Atlas of Inflammation Resolution (AIR). Mol. Aspects Med. 100894. DOI: 10.1016/j.mam.2020.100894

10.      Singh N, Eberhardt M, Wolkenhauer O, Vera J, Gupta SK. An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. BMC Bioinformatics 2020, 21 (1), 1-17. DOI: 10.1186/s12859-020-03656-6

back to staff