I am a postdoctoral researcher for the special research program RNA-REG (RNA regulation of the transcriptome) at Max F. Perutz Laboratories in Vienna, Austria. My major research interest is algorithmic bioinformatics, which I do with Ivo Hofacker's Theoretical Biochemistry group (TBI) at the University of Vienna.
My research covers different aspects of RNA bioinformatics, involving
- discrete energy landscapes of biopolymers
- prediction of RNA secondary structures
- RNA folding dynamics, RNA (re)folding pathways
- synthetic RNA biology and RNA design
- equilibrium and non-equilibrium properties of complex disordered systems
- efficient sampling strategies
- design of pipelines for next generation sequencing (NGS) analysis
I collaborate with biologists and clinical scientists in RNA-seq and transcriptome analysis projects, thereby developing software tools like ViennaNGS, a collection of Perl Modules for NGS analysis.
Alongside my day job as a research scientist, I gives lectures in algorithmic bioinformatics and Web Services at the Vienna University of Applied Sciences.
Being passionate about Linux, open source software and Web standards, I prefer C, Perl and Python for scientific coding and I have been using the TYPO3 Content Management Framework for Web-related projects for several years.
I recently started my own blog at rna-seq.at, which serves mainly as a collection of thoughts, code and snippets in the context of open source RNA bioinformatics and computational biology. The focus is not restricted to RNA-seq related bioinf issues but covers a wide spectrum of topics in theoretical RNA chemistry and biology, ranging from RNA folding and RNA design over statistical physics and energy landscape theory to synthetic biology.