Research

I studied Computer Science in Bielefeld, Germany, and received my “Diplom Informatik” with distinction in 2006. My diploma 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. In 2011, I completed my PhD in Bioinformatics and Genome Research, working on RNA secondary structure comparison by means of forest alignment in Bielefeld.
Currently, I am 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 and Robert Giegerich.
    Forest Alignment with Affine Gaps and Anchors, applied in RNA structure comparison. Submitted for publication.
  • Stefanie Schirmer and Robert Giegerich.
    Forest Alignment with Affine Gaps and Anchors. In Proceedings of CPM 2011, 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.