AlBi

We mainly offer topics from the area of algorithmic bioinformatics. These can range from more theoretical algorithmic questions to workflow development for specific bioinformatics applications.

Please feel free to propose and discuss your own topic with us.

You find most referenced student theses here: https://www.cs.hhu.de/lehrstuehle-und-arbeitsgruppen/algorithmische-bioinformatik/lehre-und-abschlussarbeiten/abschlussarbeiten/abgeschlossene-arbeiten. Otherwise ask.

• An edge-based ILP for modeling leaf venation patterns (builds on BSc thesis Mario Surlemont). Contact: Gunnar Klau
• SAT Formulation for MERIDA https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab546/6342406. Contact: Nguyen Khoa Tran
• ILP for Matrix Reordering Problem https://www.vldb.org/conf/2004/RS1P1.PDF. Contact: Nguyen Khoa Tran
• Implement an algorithm to find active modules (average Heinz) by maximizing a fractional objective function https://www.biorxiv.org/content/10.1101/2021.05.11.443638v2 Contact: Gunnar Klau
• Maximize dispersion for anticlustering using constraint programming. Builds on BSc thesis Max Diekhoff. R skills necessary/advisable. Contact: Gunnar Klau
• Spa-Typing and Flight Data: Collect Flight Data and Samples from Spa Database and look for Correlations (Check if a high volume of flights correlates to similar detected Spa-Types / Develop a framework to check correlation between flight volume and genetic information), Build on Ninas work, Contact: Philipp
• Cytoscape-Fun: Update some existing app and add feature or transpose some work we have into Cytospace e.g. leaf vein thingy, update maybe: https://github.com/ls-cwi/heinz-app, Contact: Philipp
• Backport Sven's 0-Edge-CE-Heuristic into Yoshiko Main (and thus Cytoscape App), Contact: Sven, (Philipp?)
• Using SAT to model first species counterpoint and compare to ILP implementation (Tanaka) Contact: Philipp
• Integrate/Implement CP ILP Formulations as a stand-alone application that processes MIDI or as a plugin for the scorewrite software MuseScore (Tanaka) Contact: Philipp

• Projektarbeit, very unclear outcome: https://newatlas.com/massive-attack-dna-spray-paint/56881/ Decode Sequence Massive Attack