AlBi

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Possibilities for student projects (BSc, MSc, Projektarbeit, lab rotation, ...)

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.

BSc level

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
Implementing a bi-clustering ILP and application to genomic data. Overview: overview: https://academic.oup.com/bib/article/20/4/1450/4911545 ILP: https://link.springer.com/article/10.1007/s10479-016-2261-x Contact: Gunnar Klau
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
Comparison of algorithms for affine gap cost sequence alignment. Wavefront algorithm: https://academic.oup.com/bioinformatics/article/37/4/456/5904262 Contact: Laura Kuehle
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 (Very Vague), 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
Overlap epitope vaccine design: Reformulate and re-implement the ILP proposed by Dorigatti and Schubert in https://doi.org/10.1371/journal.pcbi.1008237 using the hierarchical overlap graph (https://doi.org/10.1016/j.ipl.2019.105862). Contact: Sara Schulte
Projektarbeit, very unclear outcome: https://newatlas.com/massive-attack-dna-spray-paint/56881/ Decode Sequence Massive Attack

MSc level

Implement an ILP-based approach to enumerate common molecular fragments. Background: https://peerj.com/preprints/3250/ Contact: Gunnar Klau. NOT AVAILABLE ANYMORE