Available Bioinformatics Projects

The large variety of experiments performed at the chair requires tool, method and algorithm development in areas such as data visualization, machine learning and databases with applications ranging from basic research to clinical setups.

To apply, please send an e-mail to Dr. Matthew The with the following information:

1. type of project (BSc thesis/MSc thesis/internship/IDP)
2. what skills and/or domain knowledge you are interested in learning and/or applying
3. the project(s) you are interested in
4. your preferred start and finish time
5. attachments:
   1. CV and transcript
   2. code of a project of your choice in a zip file

Below is a selection of projects we currently have on offer. Feel free to reach out for additional projects or if you have your own project ideas.

• Data visualization and UI
  • Pathway visualization - BA, Internship
  • VueJS plotting components - BA, Internship, IDP
• Machine and deep learning
  • Kinase substrate prediction with deep learning - MA, BA, Internship
  • Similarity between cell line and patient proteome profiles - MA
• Databases
  • Spectra clustering on repository scale - MA
  • PTM integration - BA, MA, Internship, IDP
• Algorithm development
  • Decoy spectral libraries - MA
  • Match-between-runs in ProteomicsDB - MA
• Data science
  • Phosphorylation motif scoring in drug perturbation data - MA
  • Kinase activity benchmarking - MA
• Data processing pipelines
  • LIMS triggered processing - BA, Internship, IDP
  • Database search engine pipeline - BA, Internship