Summary

Cancers are heterogeneous and complex and so are the responses of the affected organisms to radiation and combination therapies, and the data (e.g. high-througput sequencing data) obtained from such systems. The key question asked in this project is: Can we develop computational methods that allow us to gain reliable knowledge from experimental or clinical data despite this high level of heterogeneity and complexity? At its core, the answer that we envision is a computational toolbox that enables researchers to integrate complex data from our systems of interest in probabilistic models. Such probabilistic models can explicitly account for uncertainty and thus for heterogeneity. The models will be used to study our systems quantitatively by Bayesian inference. Around this central modelling component, further tools can be added for data processing and complementary analyses such as ordination or clustering, resulting in data analysis pipelines for reproducible research in radiation oncology.
 

Selected Publications

Habermann D, Kharimzadeh H, Walker A, Li Y, Yang R, Kaiser R, Brumme ZL, Timm J, Roggendorf M, Hoffmann D. HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations. Bioinformatics. 2022 Mar; Available from: http://dx.doi.org/10.1093/bioinformatics/btac134.

Spassova I, Ugurel S, Kubat L, Zimmer L, Terheyden P, Mohr A, Björn Andtback H, Villabona L, Leiter U, Eigentler T, Loquai C, Hassel JC, Gambichler T, Haferkamp S, Mohr P, Pfoehler C, Heinzerling L, Gutzmer R, Utikal JS, Horny K, Schildhaus HU, Habermann D, Hoffmann D, Schadendorf D, Becker JC. Clinical and molecular characteristics associated with response to therapeutic PD-1/PD-L1 inhibition in ad vanced Merkel cell carcinoma. J Immunother Cancer. 2022;10. doi:10.1136/jitc-2021-003198.

Krysztofiak A, Szymonowicz K, Hlouschek J, Xiang K, Waterkamp C, Larafa S, Goetting I, de Celis SVR, Theiss C, Matschke V, Hoffmann D, Jendrossek V, Matschke J. Metabolism of cancer cells commonly responds to irradiation by a transient early mitochondrial shutdown. iScience. 2021 nov;24(11):103366. doi:10.1016/j.isci.2021.103366.

Tötsch N, Hoffmann D. Bayesian Data Integration Questions Classic Study on Protease Self-Digest Kinetics. ACS Omega. 2020;5:15162–15168. doi:10.1021/acsomega.0c01109.