Theses and Project Opportunities

For current theses and projects, please check the project descriptions on the right. You are always welcome to apply with your own project idea as well, or if you think that your interests and skills match my research topics!

For your application, please always attach:

• Your motivation to do this exact project
• Your research interests
• Relevant projects and skills (ideally backed by some public resource like a GitHub repository or profile)
• If you want to do a Thesis / Guided Research / Interdisciplinary Project or similar
• Optional: Your CV and your current transcript of records

Past Projects

A list of past projects under my supervision.

2025:

• Bayesian Optimization for Biomedical Laboratories: IDP for developing a biocentral plugin for bayesian optimization on protein tasks. 
  Available as part of biocentral: https://github.com/biocentral/biocentral 
  Students: Arno Claude (TUM); Shuze Liu (TUM); Yemliha Öner (TUM)
• Sustainable Protein Prediction Model Deployment: Porting existing embedding based prediction models to the maintainable ONNX format and making them available via biocentral_server.
  Available as part of biocentral_server: https://github.com/biocentral/biocentral_server 
  Cooperation with https://iteratec.com - Paula Schlötermann (iteratec GmbH), Christian Rack (iteratec GmbH), Tehseen Rug (iteratec GmbH)

Research

Software:

• Biocentral - An open biomedical data analysis software for scientists and practitioners.
  • Main GitHub: https://github.com/biocentral/biocentral
  • Backend GitHub: https://github.com/biocentral/biocentral_server
  • Web Application: https://app.biocentral.cloud/
• Biotrainer - Biological prediction models made simple.
  • GitHub: https://github.com/sacdallago/biotrainer

Libraries:

• bio_flutter - Cross-platform representation and visualization of biological data in flutter.
  • pub.dev: https://pub.dev/packages/bio_flutter
  • GitHub: https://github.com/biocentral/bio_flutter
• tutorial_system - Interactive tutorials for flutter apps, without messing up your code.
  • pub.dev: https://pub.dev/packages/tutorial_system
  • GitHub: https://github.com/biocentral/tutorial_system     

Topics:

• Scientific Software Engineering
• Accessibility, Reproducibility, Open Source Software
• Data & Model Evaluation and Validation
• Bayesian Optimization for (biomedical) Laboratories
• Protein Language Model (pLM) Distillation & Reliability
• Protein-Protein Interaction