About us

bAIome- the Center for Biomedical AI at the University Medical Center Hamburg-Eppendorf (UKE) was founded in 2019 with the mission to develop and translate Artificial Intelligence (AI) research into innovative solutions that integrate into clinical practice thereby improving and personalizing healthcare.


Team photo

The bAIome team consists of UKE faculty members and researchers with long-standing experience in developing AI methods and their application in biomedicine.

Lorenz Adlung
Lorenz AdlungDr. rer. nat.
Junior Group Leader, I. Medical Clinic and Polyclinic, UKE
Stefan Bonn
Stefan BonnProf. Dr.
Director, Institute of Medical Systems Biology, UKE
Jan Erik Gewehr
Jan Erik GewehrDr. rer. nat.
Director, Research-IT UKE
Christopher Gundler
Christopher GundlerMaster of Science
Team lead, AI applications for Health
Claus Christian Hilgetag
Claus Christian HilgetagProf. Dr.
Director, Institute of Computational Neuroscience, UKE
Stefano Panzeri
Stefano PanzeriProf. Dr.
Director, Department of excellence for neural information processing, UKE
Anna Reinicke-Vogt
Anna Reinicke-VogtDr.
Immunologist and research coordinator, UKE
Frank Ückert
Frank ÜckertProf. Dr.
Director, Institute for Applied Medical Informatics, UKE
Vadim Ustinov
Vadim Ustinov Master of Physics
Head of bAIome IT,
René Werner
René Werner PD Dr. rer. nat.
Group leader, Institute of Computational Neuroscience, UKE


bAIome provides a nucleation point for biomedical AI research at UKE and creates unique opportunities for collaborative and interdisciplinary projects to develop novel AI approaches using clinical data. At the heart of bAIome is a core AI infrastructure resource. bAIome provides consulting and planning as well as performs research and implementation of AI projects with clinical relevance.

Selected Publications

Imaging & Image analytics

Werner, René, et al. “Clinical application of breathing-adapted 4D CT: image quality comparison to conventional 4D CT.” Strahlentherapie und Onkologie (2023): 1-6. Link
Dietrich, Esther, et al. “Towards explainable end-to-end prostate cancer relapse prediction from H&E images combining self-attention multiple instance learning with a recurrent neural network” Machine Learning for Health, 38-53 Link
Ristow, Inka et al. “Evaluation of magnetic resonance imaging-based radiomics characteristics for differentiation of benign and malignant peripheral nerve sheath tumors in neurofibromatosis type 1.” Neuro-oncology vol. 24,10 (2022): 1790-1798. doi:10.1093/neuonc/noac100 Link
Schmitz, Rüdiger et al. “Artificial intelligence in GI endoscopy: stumbling blocks, gold standards and the role of endoscopy societies.” Gut vol. 71,3 (2022): 451-454. doi:10.1136/gutjnl-2020-323115 Link

Genomics & Transcriptomics

Khatri, Robin, and Stefan Bonn. “Uncertainty Estimation for Single-cell Label Transfer.” Conformal and Probabilistic Prediction with Applications. PMLR, 2022. Link
Hausmann, Fabian, et al. “DiSCERN-Deep Single Cell Expression ReconstructioN for improved cell clustering and cell subtype and state detection (preprint).” (2022). Link
Adlung, Lorenz et al. “Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells.” Cell reports vol. 36,6 (2021): 109507. doi:10.1016/j.celrep.2021.109507 Link
Adlung, Lorenz et al. “Machine learning in clinical decision making.” Med (New York, N.Y.) vol. 2,6 (2021): 642-665. doi:10.1016/j.medj.2021.04.006 Link
Marouf, Mohamed, et al. “Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks” Nature communications 11 (1), (2020): 166 Link
Menden, Kevin, et al. “Deep learning–based cell composition analysis from tissue expression profiles” Science advances 6 (30), (2022): eaba2619 Link
Adlung, L. “Cell and Molecular Biology for Non-Biologists: A short introduction into key biological concepts” Springer Berlin Heidelberg 2022 Link

Computational Neuroscience

Panzeri, Stefano et al. “The structures and functions of correlations in neural population codes.” Nature reviews. Neuroscience vol. 23,9 (2022): 551-567. doi:10.1038/s41583-022-00606-4 Link
Koren, Veronika et al. “Computational methods to study information processing in neural circuits.” Computational and structural biotechnology journal vol. 21 910-922. 11 Jan. 2023, doi:10.1016/j.csbj.2023.01.009 Link
Kira, Shinichiro et al. “A distributed and efficient population code of mixed selectivity neurons for flexible navigation decisions.” Nature communications vol. 14,1 2121. 14 Apr. 2023, doi:10.1038/s41467-023-37804-2 Link
Goulas, Alexandros et al. “Bio-instantiated recurrent neural networks: Integrating neurobiology-based network topology in artificial networks.” Neural networks : the official journal of the International Neural Network Society vol. 142 (2021): 608-618. doi:10.1016/j.neunet.2021.07.011 Link
Fakhar, Kayson, and Claus C Hilgetag. “Systematic perturbation of an artificial neural network: A step towards quantifying causal contributions in the brain.” PLoS computational biology vol. 18,6 e1010250. 17 Jun. 2022, doi:10.1371/journal.pcbi.1010250 Link
Damicelli, Fabrizio et al. “Brain connectivity meets reservoir computing.” PLoS computational biology vol. 18,11 e1010639. 16 Nov. 2022, doi:10.1371/journal.pcbi.1010639 Link

Text Mining & Electronic Health Records

Fuhlert, Patrick, et al. “Deep Learning-Based Discrete Calibrated Survival Prediction” IEEE International Conference on Digital Health (ICDH), (2022): 169-174 Link

Multi-Type Data Integration

Oller-Moreno, Sergio, et al. “Algorithmic advances in machine learning for single-cell expression analysis.” Current Opinion in Systems Biology 25 (2021): 27-33. Link
Madan, Sumit, et al. “A semantic data integration methodology for translational neurodegenerative disease research.” (2018). Link


bAIome offers a variety of courses, workshops, and one-on-one training for scientists, clinicians and students from various disciplines to become the next generation of AI experts in biomedicine.

Our teaching activities span all areas of AI applications in biomedical research. We aim at a strong focus on key questions with clinical relevance, e.g., how to extract informative features from biomedical images to inform diagnosis and treatment of diseases like prostate cancer. To answer these questions, we provide basic training of methods central to understanding, utilizing, and ultimately further developing AI applications. As such, we also teach python programming.


Students learning

With state-of-the-art medical and computational facilities, resources, and talent, bAIome is an attractive place to learn, develop, and apply biomedical AI. The flexible exchange with other academic and industry partners provides the unique opportunity for students, clinicians, and scientists to contribute to translational research for healthcare applications.


One of bAIome’s most important roles is that of a hub between the forefront of AI research, clinical demand, and biomedical application. We view our partnerships with industry as an essential ingredient and catalyst for the translation of technological advances, as a channel to spread the expertise and to bring advanced treatment options to patients. We are continuously expanding our network and welcome new innovative partners in development and exploitation of biomedical AI solutions.

For more information please contact us here.