Kliniken & Institute … Institute Pathologisches Institut… Allgemeine Pathologie … Forschung Arbeitsgruppen AG Budczies (Medical…


New technologies of molecular biology allowing comprehensive molecular profiling of biological systems are currently revolutionizing medical research. Next-generation sequencing (NGS) allows the interrogation of all base pairs of the human genome and comprehensive analysis of RNA expression. Proteomics including bulk and in situ analyses as wells as metabolomics allow profiling of proteins and of small molecules.

Our group conducts medical research based on the systems medicine paradigm of comprehensive molecular profiling. We develop models, methods and software for the analysis of molecular high-throughput data. Often, our research questions require the integration of heterogeneous data such as different layers of molecular data, histomorhphological/immunohistochemical data, clinical data and biological knowledge.    

Our research activities focus on cancer research and tissue biomarker development with typical research questions as follows: How can measurement of complex biomarkers such as tumor mutational burden (TMB) being optimized and being introduced into clinical practice? Why do some tumors respond to specific therapies (e.g. immune therapy), while other tumors do not respond and how can therapy resistance being overcome? How can the molecular alterations and mechanisms behind specific histopathological patters (e.g. of tumor cell budding) being uncovered and being made exploitable for therapeutic targeting?

Our group is responsible for administration, operation and upgrading of the IT infrastructure of the Heidelberg Molecular Pathology Center (Molekularpathologisches Zentrum, MPZ).


Cutoff Finder: Analysis and optimization of biomarker cutpoints (web app paper)
Ioncopy: Calling of copy number alterations from panel sequencing data (web app R package papers
Ionflows: Estimation of the number of flows needed for semiconductor sequencing (R package paper)
Cancerclass: Implementation of the multiple random validation protocol for cancer classification (R package paper)
Our software is for research use only. While we test our software as careful as possible, we cannot accept any liability in case of possible errors. We are grateful for bug reports and will improve the software accordingly.  


National Center for Tumor diseases, Heidelberg (NCT)
German Cancer Aid (Deutsche Krebshilfe, DKH)
Center for Personalized Medicine (Zentrum für personalisierte Medizin, ZPM)


Group leader
Prof. Dr. rer. nat. Jan Budczies (Pubmed)

Reserach scientists
Dr. rer. nat. Eugen Rempel (Pubmed)

Diplom-Bioinf. Susanne Beck (Pubmed)

PhD students
Dipl.-Phys., Dipl.-Math. Klaus Kluck (Pubmed)

M.Sc. Bioinf. Iordanis Ourailidis (Pubmed)

Eva Romanovsky, B.Sc. (Pubmed)