The workshop on RNA design organized by the RiboNets consortium will be held July 9 - 10 in Vienna. As the consortium investigates RNA designs on the three levels, in silico, in vitro and in vivo,  we invited experts in these fields to discuss our work and future plans.



The workshop takes place in the building of the Computer Science Institute at the University of Vienna (highlighted in orange on the map below).

 Venu Workshop

Faculty of Computer Science, University of Vienna, Währinger Straße 29, 1010 Vienna (please click the map for brows-able version)


More precisely it will be in Seminar room 6 at the first floor.
Follow the signs ;)



For our guests and the members of the consortium we reserved rooms in Hotel Boltzmann (5 minutes walk to the venue) and the Pension Ani Falstaff (15 minutes walk to the venue). Both places are highlighted in red on the above map. We'll book a room for you after registration.


Attending Guests:



For a detailed progam including abstracts of all contributions in PDF format please click [here].

Thursday 9.7.2015






Room is open and coffee available



9:30 – 10:00

Welcome and Introduction of RiboNets

Ilka Axmann/Sven Findeiß


10:00 – 10:45

Engineering Small Transcription Activating RNAs (STARs) [restricted access]

James Chappell

Cornell University Ithaca/United States

10:45 – 11:00

Get Coffee and Tea



11:00 – 11:45

Principles for Computational RNA Design

Peter F. Stadler

University Leipzig/Germany

11:45 – 13:15

Lunch Break



13:15 – 14:00

Aptamers for Environmental Applications (restricted access)

Beate Strehlitz

UFZ Leipzig/Germany

14:00 – 14:45

RNA-SELEX for autoinducer sensing aptamers

Sabine Schneider

RiboNets University Düsseldorf/Germany

14:45 – 15:15

Coffee Break



15:15 – 16:00

De novo RNA design approach

Stefan Hammer

RiboNets University Vienna/Austria

16:00 – 16:45

From small cyanobacterial RNA regulators to synthetic RNA device

Dennis Dienst

RiboNets University Düsseldorf/Germany


Conference Dinner and Poster Session




Design criteria for synthetic riboswitches acting on transcriptionDesign criteria for synthetic riboswitches acting on transcription

 Manja Wachsmuth

Max Plank Institut EVA Leipzig/Germany


Design of XOR riboswitches

 Stefan Badelt

University Vienna/Austria


Construction and analysis of in silico designed synthetic riboswitches (restricted access)

 Gesine Domin

University Leipzig/Germany


Modelling RNA devices in cellular context

 Stefan Hammer

University Vienna/Austria


SHAPE directed RNA folding

 Ronny Lorenz

University Vienna/Austria

Friday 10.7.2015






Room is open and coffee available



9:30 – 10:15

Dynamics of compartmentalized RNA replicator (restricted access)

Phillipe Nghe

LBC – ESPCI Paris/France

10:15 – 11:00

Prototyping of synthetic biology designs in cell free (TX-TL) system

Paul S. Freemont

Imperial College London/United Kingdom

11:00 – 11:15

Get Coffee and Tea



11:15 – 12:00

In vitro apporaches to investigate RNA riboregulators (restricted access)

Andre Estevez-Torres

RiboNets CNRS Paris/France

12:00 – 14:15

Lunch Break



14:15 – 15:00

Synthetic RNA Networks for In Vivo ComputationSynthetic RNA Networks for In Vivo Computation (restricted access)

Alexander Green

Arizona State University/United States

15:00 – 15:30

Coffee Break



15:30 – 17:00

Open Discussion




Concluding Remarks

Ilka Axmann






Apr 2017: RNAblueprint accepted

Our in silico RNA sequence design framework, comprised of a powerful sequence sampler (RNAblueprint) and a Python wrapper (RNAsketch), got accepted for publication in Bioinformatics and is available on GitHub.

Dec 2016: Riboswitch publication

We successfuly published our work on Riboswitch design together with Mario Moerl and Peter F. Stadler from University Leipzig in Nucleic Acids Research.

Oct 2016: RNAblueprint online

RNAblueprint, a software to fairly sample nucleic acid sequences compatible with multiple structural and sequence constraints, is now online. The corresponding publication has been submitted to Bioinformatics.

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