Personal website of Felix Kühnl.

After finishing my M. Sc. in Bioinformatics in March 2016, I am now a PhD student in the group of Peter F. Stadler. He holds the Chair for Bioinformatics at Leipzig University. You can find my CV here.

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

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.

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

waterfall: Partial exploration of RNA landscapes.

This script implements a novel method to explore the energy landscape of a given RNA molecule. Since the conformation space of an RNA grows exponentially with that RNA's sequence length, a complete enumeration of all possible structures is infeasible even for short molecules. By using methods such as Wuchty's algorithm, it is possible to enumerate only structures up to an energy threshold. Yet, one is often interested in structures that lie beyond all feasible thresholds, and so a heuristic exploration of the landscape is required. waterfall enables the user to specify a set of interesting RNA structures for a given sequence, and explores their neighborhood by iteratively flooding their gradient basins up to a specified energy level. If it finds contact states that lead to other basins, it follows them until it reaches low energy regions of the landscape. This way, the interesting input structures are connected to the part of the landscape which can easily be enumerated, allowing for accurate kinetic simulations including arbitrary structures.

Download coming soon!


This is a list of my publications.

  • 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.


To contact me, just write me an e-mail. My phone number is +49 341 97 16678. The postal address of our institute can be found here.