Research

I studied Computer Science in Bielefeld, Germany, and received my “Diplom Informatik” with distinction in 2006. My project was a typechecker for the compiler of the programming language ADP, which is suited for Dynamic Programming problems, a frequent type of problems in Bioinformatics. My talk at Strangeloop gives an introduction to this topic.

In 2011, I completed my PhD in Bioinformatics and Genome Research, working on RNA secondary structure comparison by means of forest alignment in Bielefeld. Check out my thesis if you are curious about comparing forests. Until 2015, I was a postdoctoral researcher at the Institute for Research in Immunology and Cancer of Université de Montréal.

My research interests include RNA secondary structure analysis, alignment and folding; dynamic programming and efficient solution of Bioinformatics problems; languages and compiler construction.

Publications

• Stefanie Schirmer, Yann Ponty, and Robert Giegerich. Introduction to RNA Secondary Structure Comparison. Bookchapter, in: Jan Gorodkin and Walter L. Ruzzo (Eds.). RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Series: Methods in Molecular Biology, Vol. 1097, Humana Press, 2014.

• Paul Dallaire, Stefanie Schirmer, François Major. Navigating through the MC-Flashfold 2D Suboptimal Solution Maze using simple Structural Transformation Rules. In Proceedings of RNA 2013, The 18th Annual Meeting of the RNA Society, 2013.

• Stefanie Schirmer and Robert Giegerich. Forest Alignment with Affine Gaps and Anchors, applied in RNA Structure Comparison. Theoretical Computer Science 483: 51–67, 2013.

• Stefanie Schirmer and Robert Giegerich. Forest Alignment with Affine Gaps and Anchors. In Proceedings of CPM 2011, The 22nd Annual Symposium of Combinatorial Pattern Matching, 2011.

• Jan Anlauff, Erik Weitnauer, Alexander Lehnhardt, Stefanie Schirmer, Sebastian Zehe, and Keywan Tonekaboni. An outdoor skateboarding video game – introducing equipment based physical interfaces for augmented reality games. In Proceedings of International Conference on Advances in Computer Entertainment Technology, 2010.

• Florian Grond, Stefan Janssen, Stefanie Schirmer, and Thomas Hermann. Browsing RNA structures by interactive sonification. In Proceedings of ISon 2010, 2010.

• Andreas Bremges, Stefanie Schirmer, and Robert Giegerich. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics, 11:222, 2010.

• Stefanie Schirmer. Tree alignment of RNA secondary structures with affine gap costs. In Proceedings of Bioinformatics Research and Education Workshop, 2008.

• Stefanie Schirmer. In search of the best model for RNA structure comparison. In Proceedings of Bioinformatics Research and Education Workshop, 2007.