Personal website of Felix Kühnl.

After finishing my MSc in Bioinformatics in March 2016, I was a PhD student and, after my graduation in 2022, a postdoc in the group of Peter F. Stadler. He holds the Chair for Bioinformatics at Leipzig University. In 2023, I left academia to seek new challenges in the industry.

My main research interests are the design of artificial RNA molecules as well as RNA folding kinetics in general.

My PhD thesis is concerned with various aspects RNA folding, including the design of transcriptional riboswitches, statistics of RNA structures, and quality control of folding models.

In my master's thesis, I modeled the folding kinetics of RNA–ligand interaction processes. Meanwhile, I was involved in a project to identify protein binding motifs in long non-coding RNAs (lncRNAs) with Lydia Müller.

On this web page you can find my software, a list of my publications and other hopefully useful information. Should you have any question, feel free to contact me.


Here you can find a list of my software. These tools are free software published under the GNU General Public License.

BarMap-QA – Cotranscriptional folding with quality assurance.

BarMap-QA is a ready-to-use pipeline for conducting cotranscriptional folding analyses of short to medium-sized RNA molecules. For more information, please visit the official homepage.

RNA–Ligand Interaction and Riboswitch Kinetics

This is a pipeline capable of simulating the folding kinetics of an RNA molecule in the presence of a binding ligand. Assuming ligand excess and a single structural binding motif, the kinetics are computed by solving a coarse-grained Markov process via diagonalization of its rate matrix. The coarse graining is based on the idea of gradient basins in the energy landscape of the RNA. This script allows an in silico analysis, e.g. of riboswitches, that yields much more information than simple thermodynamic calculations that cannot consider any kinetic effects.

This software is now available via Bioconda . To install it, simply run the following command:

conda install kinsimriboswitch

Last update: 2018-10-02, 17:19


This is a list of my publications. Please also have a look at my ORCID record.

  • Felix Kühnl (9 May 2022):
    The Folding Kinetics of RNA. From Folding Simulations to the Design of Synthetic Molecules.
    PhD thesis.
    Publication server
  • Sven Findeiß, Stefan Hammer, Michael T. Wolfinger,
    Felix Kühnl, Christoph Flamm, Ivo L. Hofacker (1 Jul 2018):
    In silico design of ligand triggered RNA switches.
    Methods Vol. 143, pp. 90-101, Elsevier.
  • Felix Kühnl, Peter F. Stadler, Sebastian Will (2017)
    Tractable RNA–ligand interaction kinetics.
    BMC Bioinformatics 18.12 (2017): 424.
  • Felix Kühnl, Peter F. Stadler and Sebastian Will (2016):
    Tractable Kinetics of RNA–Ligand Interaction.
    ISBRA 2016 Proceedings, p. 337f, Springer.
  • Felix Kühnl (2016):
    Folding Kinetics of Riboswitches – A tractable concentration-dependent approach.
    Master's Thesis. Supervisors: Peter F. Stadler, Sebastian Will.
  • Felix Kühnl (2014):
    orthoDeprime: A Tool for Heuristic Cograph Editing on Estimated Orthology Graphs.
    Bachelor's Thesis. Supervisors: Peter F. Stadler, Maribel Hernandez-Rosales.


If you wish to contact me, please feel free to write me an e-mail.