Theses and Project Opportunities

You are always welcome to apply for a collaboration with your own project 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 - Biomedical data, from lab to paper.
  • Frontend GitHub: https://github.com/biocentral/biocentral
  • Backend GitHub: https://github.com/biocentral/biocentral_server
  • Programmatic APIs GitHub: https://github.com/biocentral/biocentral_api
  • Web Application: https://app.biocentral.cloud/
  • Rostlab Server: https://biocentral.rostlab.org/
• 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    
• ranking_system - A flexible and powerful ranking system for Flutter applications.
  • pub.dev: https://pub.dev/packages/ranking_system
  • GitHub: https://github.com/biocentral/ranking_system 

Topics:

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

Publications

• Franz, S., Olenyi, T., Schloetermann, P., Smaoui, A., Jimenez Soto, L. F., & Rost, B. (2025). biocentral: embedding-based protein predictions. bioRxiv. https://doi.org/10.1101/2025.11.21.689449
• Labaca-Castro, R., Franz, S., & Rodosek, G. D. (2021). AIMED-RL: Exploring Adversarial Malware Examples with Reinforcement Learning. In Machine Learning and Knowledge Discovery in Databases. Applied Data Science Track (pp. 37–52). Springer International Publishing. doi.org/10.1007/978-3-030-86514-6_3