Applied Bioinformatics

The Applied Bioinformatics working group in the Medical Bioinformatics research area at the MPC is headed by Dr. Julian Uszkoreit. In close collaboration with experimental research groups we develop new methods and algorithms and apply them mainly to mass spectrometric data from proteomics to answer questions from the life sciences. Our group uses current methods of software development and deployment (e.g. workflow environments, cloud computing, deep learning, containerization, orchestration), as well as the high-performance hardware equipment of the MPC and the PRODI research building to address project-specific questions but also to solve fundamental problems of proteomics. All our tools and methods are made available to the community in a user-friendly way and as open source.
Our current projects include:


  • Deep-Learning to improve the identification of peptide spectra
  • Detection of peptide variants in proteomics data
  • Flexible and comprehensively parameterizable protein inference based on the peptide identifications of various MS/MS analysis algorithms, also for quantitative data
  • Quality control of mass spectrometric data
  • Reanalysis of existing data sets with new methods and under new aspects
  • Connection of our methods as analysis nodes in KNIME
  • Participation in Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO)
  • Participation in EuBIC - European Bioinformatics Community for Mass Spectrometry
  • The new methods and algorithms are incorporated into the platform technology proteomics at PRODI, the Center for Protein Diagnostics. In the future, oncological and neurodegenerative diseases should be diagnosed better and earlier - if possible before clinical symptoms occur.

In addition to the research activities, members of the working group operate the scientific server infrastructure of the Medical Proteome Center.

Working Group Leader

Dr. Julian Uszkoreit


Ruhr-Universität Bochum
ProDi, Raum E2.240
Gesundheitscampus 4
D-44801 Bochum

Tel: +49 234 32 18109