Publications:

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!), 14th 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, 31th TBI Winterseminar Bled, 2016 (Talk) [PDF]

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

  • Axmann IACyanobacteria’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 CRiboswitches - Design and Modelling, 30th 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)

 

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