consortium

We, the FET Young Explorers, Andre Estévez-Torres, Ilka Axmann and Sven Findeiß, successfully raised EU funding for the RiboNets project. After three and half years RiboNets ended in April 2017. Our achievements, including publications and developed software, are listed below.

Our multi-disciplinary approach blended the three layers of in silico, in vitro and in vivo analysis and fostered the successful engineering of functional RNA molecules.  Please find more details about the project and the consortium at the corresponding sub pages.

 

The workshop on RNA design organized by the RiboNets consortium will be held from

June 14 - 15  2017 in Duesseldorf (Germany).

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 RiboNets consortium is made up of three partners actually located at four universities. A short description of each member is given below.

 

University of Vienna

 

UNI-Logo RGB 01The Bioinformatics and Computational Biology (BCB) research group at University of Vienna, Austria is headed by two professors, i.e. Ivo L. Hofacker and Arndt von Haeseler, and works on the interdisciplinary bioinformatics research field. The research activity of the group of Ivo L. Hofacker at the Institute of Theoretical Chemistry at University of Vienna ranges from classical quantum mechanical calculations, accurate calculations on structures and activities of small molecules, development of theoretical methods for drug design to investigations of evolution and bioinformatics of RNA. It has especially a long standing expertise in RNA research ranging from molecule design to genome wide detection of non-coding RNA elements. With the development and ongoing improvement as well as constant extension of the Vienna RNA  package the group provides one of the widely used software suites for RNA structure prediction and analysis. 

 

Key people: Sven Findeiß, Christoph Flamm and Stefan Hammer

 

Heinrich Heine University Düsseldorf

 

uni duesseldorf logoThe Cluster of Excellence on Plant Sciences (CEPLAS) is a joint initiative of Heinrich Heine University, University of Cologne, Max Planck Institute for Plant Breeding Research and Forschungszentrum Jülich. It applies a new approach that is driven by evolutionary analysis and synthetic biology. CEPLAS aims to understand the genetic architecture and the regulatory networks of four important complex traits at the level of a quantitative model followed by the synthesis of the trait’s modules and sub-modules. The Institute for Synthetic Microbiology, headed by Ilka Axmann, is embedded in CEPLAS’ Research Area D - Plant metabolism: from biotic challenges to synthetic biology. We are aiming at smart, automated and dynamic control of synthetic metabolic pathways in microorganisms using synthetic RNA-devices and RNA-based metabolite-sensors. Particular focus is placed on the engineering of cyanobacteria as a future host for sustainable biotechnology.

 

Key people: Ilka Axmann and Dennis Dienst

 

Humboldt University of Berlin

 

husiegel bwThe Institute of Theoretical Biology (ITB), being at the interface between Charité and Humboldt University Berlin, is one of the central hubs for mathematical modelling of biological systems in Germany, with six research groups investigating molecular networks through mathematical modelling. 

 

Key people: Ilka Axmann, Dennis Dienst and Tim Kolmsee

 

Centre national de la recherché scientifique

 

logocnrsThe Laboratoire de photonique et de nanostructures (LPN), belonging to the Centre national de la recherché scientifique (CNRS), with 47 permanent research staff, 38 technical staff and 1000 m2 of clean room is one of the major micro- and nanofabrication facilities in France. LPN carries out its research activities in the nanosciences, at the cross-roads of quantum optics and electronics, of physics, chemistry and biology, of materials science and device physics. LPN develops the new technologies and concepts that initiate innovation both in basic and in applied science. It has been a pioneer in France in merging microfabrication chemistry and biology, notably in the field of microfluidics, which is central to this project.

 

Key people: Andre Estévez-Torres and Jonathan Lee

News

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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