Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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TBI - Stefan Hammer

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I studied Genetics and Microbiology at the University of Vienna and started as a PhD student at the TBI in fall 2012.
As I am very interested in RNA design and synthetic biology my main project at the moment is to create a tool able to design context-sensitive riboswitches with advanced prescribed properties and functions.

Multiple target sequence design

Picture We developed RNAblueprint, a C++ library implementing a graph coloring approach to uniformly sample sequences compatible to structural and sequence constraints from the typically huge solution space. Fair sampling from the solution space makes optimization runs much more performant and raises the probability to find better solutions. Scripting interfaces allow to easily adapt existing code to new scenarios which makes the whole design process very universal and flexible. A python module RNAsketch provides code for glueing together RNAblueprint and structure prediction packages and to provide precoded optimization methods.

More information and source code:
https://github.com/ViennaRNA/
https://viennarna.github.io/RNAblueprint/
https://viennarna.github.io/RNAsketch/

RNAdevices Database

This database is mainly intended to summarize RNA sequence designs that are interesting for our Ribonets Project. As we extract and summarize the essential information of each publication and offer an easy way to download it, the content might be helpful for other researches as well.
In the future we plan to extend the database to metabolite and peptide induced designs.

http://ribonets.eu/RNAdevices/

ODE system to model RNA devices

As part of the Ribonets Project we built an ODE system describing designed or natural riboswitches in the context of transcription and translation.
The system created by the Keasling lab was therefore 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

Vienna RNA Packaging

For a better user experience, I started to maintain Debian and Ubuntu packages for our Vienna RNA Package. Furthermore, there exists a Launchpad PPA for our Ubuntu-users.
The packages can be downloaded here, while the ppa is hosted at https://launchpad.net/~j-4/+archive/vienna-rna/.
If you are interested in some statistics about the ppa, check out the ppastats.

Publication/Poster List

Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
RNAblueprint: Flexible multiple target nucleic acid sequence design
Bioinformatics (2017), doi:10.1093/bioinformatics/btx263, PDF (7.5MB)
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
Flexible and universal multiple target nucleic acid sequence design
Poster (2016), PDF (2.2MB)
Stefan Hammer, Sven Findeiß, Stefanie Hertel, Christoph Flamm, Ivo L. Hofacker
Modelling RNA devices in a cellular context
Poster (2015), PDF (624kb)
Peter Kerpedjiev, Stefan Hammer and Ivo L. Hofacker
forna (force-directed RNA): Simple and Effective Online RNA Secondary Structure Diagrams
Bioinformatics (2015), doi:10.1093/bioinformatics/btv372, PDF (274kb)
Stefan Badelt, Stefan Hammer, Christoph Flamm, Ivo L Hofacker
Thermodynamic and kinetic folding of Riboswitches
Methods in Enzymology, Volume 554 (2015), doi:10.1016/bs.mie.2014.10.060, PDF (404.1kb)
Stefan Hammer, Sven Findeiß, Ivo L. Hofacker, Christoph Flamm
Engineering of RNA based devices for complex regulatory networks
Poster (2014), PDF (901.4kb)
Christian Höner zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler
Computational design of RNAs with complex energy landscapes
Biopolymers (2013), 1097-0282, doi:10.1002/bip.22337, PDF (659 kb)
Stefan Hammer
Target tissues of melatonin and PDF in Platynereis
Wien, Univ. (2012), Dipl.-Arb., http://ubdata.univie.ac.at/AC10863946