Publications:

• Hammer S, Guenzel C, Moerl M and Findeiß S, Evolving methods for rational de novo design of functional RNA molecules, 2019, doi:10.1016/j.ymeth.2019.04.022
• Hammer S, Wang W, Will S and Ponty Y, Fixed-parameter tractable sampling for RNA design with multiple target structures, BMC Bioinformatics, 2019, doi:10.1186/s12859-019-2784-7
• Findeiß S, Hammer S, Wolfinger Michael T, Kühnel Felix, Flamm Christoph, Hofacker Ivo L, In silico design of ligand triggered RNA switches, Methods, 2018, doi:10.1021/acssynbio.7b00387
• Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Jaramillo A, Findeiß S, Axmann I and Estevez-Torres A, Quantitative characterization of translational riboregulators using an in vitro transcription-translation system, ACS Synth Bio, 2018, doi:10.1021/acssynbio.7b00387
  
• Hammer S, Yann Ponty, Wei Wang, Sebastian Will, Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures, RECOMB'18
• Findeiß S, Etzel M, Will S, Mörl M, Stadler PF, Design of Artificial Riboswitches as Biosensors, Sensor, 2017, doi:10.3390/s17091990.
• Hammer S, Tschiatschek B, Flamm C, Hofacker IL and Findeiß S, RNAblueprint: Flexible and universal multiple target nucleic acid sequence design. Bioinformatics, 2017, doi:10.1093/bioinformatics/btx263
• Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF and Mörl M, Applicability of a computational design approach for synthetic riboswitches, Nucleic Acids Res., 2016, doi:10.1093/nar/gkw1267
• Lee Tin Wah J, David C, Rudiuk S, Baigl D and Estevez-Torres A, Observing and controlling the folding pathway of DNA origami at the nanoscale, ACS Nano, 2016, doi:10.1021/acsnano.5b05972
• Kerpedjiev P, Hammer S, Hofacker IL, forna (force-directed RNA): Simple and Effective Online RNA Secondary Structure Diagrams, Bioinformatics, 2015, doi:10.1093/bioinformatics/btv372
• Wachsmuth M, Lorenz R, Serfling R, Findeiß S, Stadler PF and Mörl M, Design criteria for optimized synthetic transcriptional riboswitches, Nucleic Acids Res., 2015, doi:10.1080/15476286.2015.1017235.
• Findeiß S, Wachsmuth M, Mörl M and Stadler PF, Design of Transcription Regulating Riboswitches, Methods in Enzymology, 2015, doi:10.1016/bs.mie.2014.10.029.
• Badelt S, Hammer S, Flamm C, Hofacker IL, Thermodynamic and kinetic folding of Riboswitches, Methods in Enzymology, 2015, doi:10.1016/bs.mie.2014.10.060.
• Badelt S, Flamm C, Ivo L Hofacker IL, Computational design of a circular RNA with prion-like behaviour. In: Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFe 14). Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod Lipson (Eds.). MIT Press, pp 565-568, 2014, doi:10.7551/978-0-262-32621-6-ch091
• Andersen JL, Flamm C, Hanczyc MM, Merkle D, Towards an optimal DNA-Templated Molecular Assembler. In: Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFe 14). Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod Lipson (Eds.). MIT Press, 14:557-564, 2014, doi:10.7551/978-0-262-32621-6-ch090
• Mann M, Kucharik M, Flamm C and Wolfinger MT, Memory-efficient RNA energy landscape exploration. Bioinformatics, 2014, doi:10.1093/bioinformatics/btu337

Software/Links:

• Our software tool, RNAblueprint, to fairly sample nucleic acid sequences compatible with multiple structural and sequence constraints is available here on github. Furthermore a python module to design RNA molecules using RNAblueprint, ViennaRNA and the NUPCK package can be found here.
• Our RNAdevices database summarizing published designs is available. It is currently resticted to purely RNA based designs.
• ODE systems implementing essential cellular process, i.e. transcription, translation and degradation, to model RNA based switches are available here on github.

Workshop:

We successfully organized two workshops on RNA design. One was held in Vienna and the other in Duesseldorf.

Presentations:

• Hammer S, Findeiß S, Flamm C, Hofacker IL, Design of translationaly controled artifical gene regulation (and more!), 14^th Herbstseminar, Doubice 2016 (Talk) [HTML]

• Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Findeiß S, Axmann IM, Estevez-Torres A, Cell-free characterization of RNA translational regulators,  22nd International Conference on DNA Computing and Molecular Programming, Munich, Germany (Poster)

• Hammer S, Findeiß S, Tschiatschek B, Flamm C, Hofacker IL, Flexible and universal multiple target sequence design,  DK Retreat Pamhagen, 2016 (Poster) [PDF]

• Axmann IA, Synthetic RNA-based control units for balanced triterpene biosynthesis in cyanobacteria, Annual conference of the Association for General and Applied Microbiology (VAAM), Jena, 2016 (Poster)

• Dienst D, Towards synthetic RNA devices in cyanobacteria, Annual conference of the Association for General and Applied Microbiology (VAAM), Jena, 2016 (Poster)

• Hammer S, Design of context-sensitive, multi-stable RNA switches, Progress Report, Vienna, 2016 (Talk) [PDF]

• Hammer S, Findeiß S, Tschiatschek B, Flamm C, Hofacker IL, Flexible and universal multiple target sequence design, 31^th TBI Winterseminar Bled, 2016 (Talk) [PDF]

• Hammer S, Findeiß S, Flamm C, Hofacker IL, RNAdesign library, 13^th Herbstseminar Doubice, 2015 (Talk) [PDF]

• Axmann IA,  Cyanobacteria’s specific features: non-standard circadian clocks and plenty of antisense RNAs, Plants and People 2015, MPI Potsdam/Golm (Talk)
• Axmann IA, Programming semi-synthetic Triterpene Biosynthesis Pathways in Cyanobacteria using synthetic RNA-based devices, CEPLAS retreat 2015, Wermelskirchen, Germany (Talk)

• Hammer S, Findeiß S, Hertel S, Flamm C, Hofacker IL, Modeling RNA devices in a cellular context, RNA DK retreat Retz, 2015 (Poster) [PDF]

• Hueren V, Kranz S, Loeschke A, Schneider S, Axmann IA, Dienst D, Towards synthetic RNA regulators, 15th international symposium on phototrophic Prokaryotes, Tuebingen, 2015 (Poster)

• Schneider S, 6S RNA, 15th international symposium on phototrophic Prokaryotes, Tuebingen, 2015 (Poster)[PDF]

• Dienst D, Schneider S, Jablonski J, Schmelling N, Kolmsee T, Axmann IA, Towards synthetic RNA regulators, Annual conference of the Association for General and Applied Microbiology (VAAM), Marburg, 2015 (Poster)

• Hammer S, Findeiß S, Flamm C, Riboswitches - Design and Modelling, 30^th TBI Winterseminar Bled, 2015 (Talk) [PDF]

• Hammer S, Findeiß S,  Hofacker IL, Flamm C, Engineering of RNA based devices for complex regulatroy networks, RNA DK retreat Retz, 2014 (Poster) [PDF]

• Lee Tin Wah J and Estevez-Torres A, In-vitro testing and characterization of nucleic acid structures and networks, International Synthetic and Systems Biology Summer School,  2014 (Poster) [PDF]

• Dienst D, Synthetic RNA-based devices, ESF Conference Biology of plastids – towards a blueprint for synthetic organelles, 2014 (Talk) [PDF]

• David C, Lee Tin Wah J and Estevez-Torres A, Folding pathway of DNA nanostructures at the single molecule level, 20th international conference on DNA Computing and Molecular Programming, Kyoto, Japan, 2014 (Talk)