Currently, I am a
PostDoc researcher in the group of Peter
Stadler at University
Leipzig. I received my
PhD in molecular biology at the Bioinformatics
and Computational Biology/Theoretical
Biochemistry research group
in Vienna after studying Genetics and Microbiology at the University
My main research interest lies in designing functional RNA molecules for synthetic biology applications. Therefore, I focus on connecting bioinformatics and wet-lab such that the whole design approach from predictive model generation, computational design to experimental verification and characterization of the obtained candidates can be advanced.
Finding RNA sequences that fulfill a desired function in the cellular context is a complex task that can be computationally solved by combining multiple methods. Due to the properties of the solution landscape, it is crucial to sample RNA sequences given various necessary constraints, e.g., the secondary target structures. We developed RNAblueprint, a C++ library which implements a graph coloring approach to uniformly sample sequences compatible to structural and sequence constraints from the typically huge solution space. The successor, RNARedPrint, solves the same task in a more general fashion by applying dynamic programming over a tree decomposition to achieve Boltzmann weighted sampling of desired sequence candidates.
Typically, the various RNA desig goals are specified by formulating an objective function, which is used for solving an optimization problem. Using structure prediction and thermodynamic models, we developed multiple objective functions in order to obtain RNA devices with specific functionality. These objectives are implemented in the python module RNAsketch, which also provides precoded optimization methods, as well as code to glue RNAblueprint, RNARedPrint, and structure prediction packages together.
An artificial RNA molecule needs to interact with the cellular environment in order to be produced and to be able to fulfill its desired tasks. Therefore, we built an ODE system describing designed or natural riboswitches in the context of transcription and translation as part of the Ribonets Project. The system created by the Keasling lab was minimized and adapted to model RNA devices such as translational and transcriptional ON or OFF switches. To share these models we chose to use the Systems Biology Markup Language (SBML).
More information and details: https://github.com/ribonets/rnadev-models
Peter and I developed forna, a RNA secondary structure visualization tool using a force directed graph layout. This tool is capable of not only drawing nice layouts for huge structures, but also of projecting pseudoknots and secondary structures of PDB files including protein interactions.
I set up a database which collects artificial RNAs, their implemented regulatory mechanism and conducted experimental validation experiments. This database facilitates data-collection from literature and helps to organize previous RNA design attempts. It is built using MySQL and Xataface, thus human as well as machine readable input and output is possible. This project was part of the Ribonets Project.
To provide a better user experience for bioinformatic tools, I started to construct and maintain various Bioconda packages. Bioconda is a channel for the conda package manager specializing in bioinformatics software. It provides packaging recipes and a build system to create a repository countless software packages used for biological purposes.
Theoretical Biochemistry Group, Bioinformatics and Computational Biology
Thesis title: Design of context-sensitive, multi-stable RNA molecules Supervisor: Ivo L. Hofacker Graduated with highest honors on April 26th, 2018
Genetics and Microbiology, specialization in Bioinformatics, Developmental Biology and Immunology
Thesis title: Target tissues of melatonin and PDF in Platynereis Supervisor: Florian Raible Graduated with hightest honors on June 5th, 2012